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Cena made his television debut answering an open challenge by Kurt Angle on June 27, 2002. Inspired by a speech given by WWE Chairman Vince McMahon to the rising stars of the company, exhorting them to show "ruthless aggression" to earn a place among the legends, Cena took advantage of the opportunity and almost beat Angle kicking out of his finishing move, the Angle Slam and enduring the ankle lock submission hold. Cena ultimately lost to a hard amateur wrestling-style pin. Following the near-win, Cena became a fan favorite and started feuding with Chris Jericho. In October, Cena and Billy Kidman took part in a tag team tournament to crown the first WWE Tag Team Champions of the SmackDown! brand, losing in the first round. The next week, Cena turned on and attacked Kidman, blaming him for their loss, becoming a villain.

Shortly after the Kidman attack, on a Halloween themed episode of SmackDown, Cena dressed as Vanilla Ice performing a freestyle rap. The next week, Cena received a new character: a rapper who cut promos while rhyming. As the gimmick grew, Cena began adopting a variant of the 1980s WWF logo — dropping the "F" — as his "signature symbol", along with the slogan "Word Life". Moreover, he was joined by an enforcer, Bull Buchanan, who was rechristened B-2 (also written B² and pronounced "B-Squared"). Buchanan was later replaced by Red Dogg, until he was sent to the Raw brand in February.

For the first half of 2003, Cena sought the WWE Championship and chased the reigning champion, Brock Lesnar, performing weekly "freestyles" challenging him to matches. During the feud, Cena unveiled a new finishing maneuver: the FU, a Fireman's carry powerslam, named to mock Lesnar's F-5. Cena won a number one contenders tournament against Lesnar at Backlash. However, Cena was defeated by Lesnar. At the end of the year, Cena became a fan favorite again when he joined Kurt Angle as a member of his team at Survivor Series.

In early 2004, Cena participated in the Royal Rumble match at the 2004 Royal Rumble, making it to the final six before being eliminated by Big Show and the Match being won by Chris Benoit. The Royal Rumble elimination led to a feud with Big Show, which Cena won the United States Championship from Big Show at WrestleMania XX. During his reign, Cena came into contention with SmackDown General Manager Kurt Angle over issues arising with René Duprée and Torrie Wilson. The reign ended almost four months later, when he was stripped of the belt on July 8 by Angle after he accidentally knocked him over, thus attacking an official. Cena won the championship back defeating Booker T in a best of five series that culminated at No Mercy, only to lose it to the debuting Carlito Caribbean Cool the next week. After the loss to Carlito, the duo began a feud, which Cena was stabbed in the kidney while at a Boston-area nightclub by Carlito's bodyguard, Jesús. In November, Cena won the United States Championship back from Carlito debuting a "custom made" spinner-style championship belt.

Cena took part in the 2005 Royal Rumble match, making it to the final two. Cena and Raw brand wrestler Batista went over the top rope at the same time, ostensibly ending the match. Vince McMahon, however, appeared on stage and re-started the match in sudden death rules, with Batista eventually eliminating Cena. The next month, Cena defeated Kurt Angle to earn a spot in the SmackDown brand's WrestleMania 21 main event match, beginning a feud with WWE Champion John "Bradshaw" Layfield (JBL) and his Cabinet in the process. In the early stages of the feud, Cena lost his US belt to Cabinet member Orlando Jordan, who proceeded to "blow up" the spinner championship with JBL and returning a more traditional style belt. Cena defeated JBL at WrestleMania winning the WWE Championship, giving Cena his first world championship. Cena then had a spinner WWE Championship belt made, while JBL took the original belt and claimed to still be WWE Champion, until Cena reclaimed the original belt in an "I Quit" match at Judgment Day.

Cena was drafted to the Raw brand on the June 6, 2005, becoming the first wrestler selected by General Manager Eric Bischoff in the annual draft lottery. Cena immediately entered a feud with Bischoff, after refusing to participate in the "war" against the Extreme Championship Wrestling (ECW) roster at One Night Stand. With Bischoff vowing to make Cena's stint on Raw difficult, he hand picked Jericho to take Cena's championship from him. During their feud, even though Cena was portrayed as the fan favorite and Jericho as the villain, a vocal section of live crowds, nonetheless, were booing Cena during their matches. More crowds followed suit during Cena's next feud with Kurt Angle, who took over as Bischoff's hand-picked number-one contender after Cena defeated Jericho in a You're Fired match on the August 22 Raw. As the feud continued and the dissenters grew more vocal, sometimes seeming to outnumber fans by wide margins, the announce team was forced to acknowledge the booing on television and began calling Cena a "controversial champion", claiming some people disliking him on account of his "in-ring style" and his chosen fashion. Despite the mixed and negative reactions, Cena held on to his championship through his feud with Angle, losing to him by disqualification – which titles do not change hands in WWE – at Unforgiven and pinning him at Survivor Series. The feud with Angle also saw Cena add a secondary, submission based, finishing maneuver – the STF (a Stepover Toehold Sleeper, though named for a Stepover Toehold Facelock) – when he was put into a Triple Threat Submissions Only match on the November 28 Raw.

Cena lost the WWE Championship at New Year's Revolution, but not in the Elimination Chamber match that he had been advertised to participate in beforehand. Instead, immediately after winning the Elimination Chamber, he was forced into a match against Edge, who cashed in his Money in the Bank contract – a "guaranteed title match for the WWE Champion at a time and place of the owners choosing." After two quick spears pinned Cena, winning the championship. Three weeks later, Cena won the championship back at the Royal Rumble. After winning the championship, Cena began feuding with Triple H, which the crowd began booing Cena and cheering the intended villain, Triple H. Cena beat Triple H at Wrestlemania 22 to retain his WWE Title. The negative reaction towards Cena intensified when facing Rob Van Dam at One Night Stand. Taking place in front of a crowd of mostly "old school" ECW fans at the Hammerstein Ballroom, when he began performing different moves into the match, the fans began chanting "You still suck". Cena lost the WWE Championship at One Night Stand, with Van Dam pinning Cena after interference from Edge.

In July, after Edge won the championship from Van Dam in a Triple Threat match that also involved Cena, re-ignited the feud between him and Cena from earlier in the year. After Edge went about retaining the title by dubious means – getting himself disqualified (for which Championships do not change hands) and using brass knuckles – he introduced his own version of Cena's "custom" belt, this one with his logo placed on the spinner. Cena eventually won the championship back in a Tables, Ladders, and Chairs match at Unforgiven. The match had an added stipulation that had Cena lost he would leave the Raw brand and go to SmackDown. Cena returned his version of the spinner belt on the next night's Raw.

On the heels of his feud with Edge, Cena was placed in an inter-brand angle to determine the "Champion of Champions" – or which was the most dominant champion in WWE's three brands. Cena, the World Heavyweight Champion King Booker, and the ECW World Champion The Big Show engaged in a mini-feud leading to a Triple Threat match at Cyber Sunday, with the viewers voting on which of the three championships would be placed on the line. At the same time, Cena became involved in a storyline with non-wrestler Kevin Federline, when he began appearing on Raw with Johnny Nitro and Melina. After getting into a physical altercation with Federline on Raw, Federline appeared at Cyber Sunday to hit Cena with the World Heavyweight Championship during the match, helping King Booker retain his championship. 2006 ended with Cena beginning a feud with the undefeated Umaga over the WWE Championship, while 2007 began with the end of his storyline with Kevin Federline. On the first Raw of the new year, Cena was pinned by Federline with an assist from Umaga, although later in the night he was able to get his hands on Federline performing an FU on him.

One night after the Royal Rumble, an impromptu team of Cena and Shawn Michaels defeated Rated-RKO (Edge and Randy Orton) for the World Tag Team Championship, making Cena a double champion. On the April 2 episode of Raw, after losing a WWE Championship match to Cena at WrestleMania 23, Michaels turned on Cena, costing them the championship in the second of two 10 team battles royals, by throwing Cena over the top rope and eliminating the team. The Hardys (Matt and Jeff) eventually won the match and the championship. For the rest of the month, Cena feuded with Michaels, Orton, and Edge until The Great Khali declared his intentions to challenge for Cena's championship attacking and "laying out" all three of the top contenders before assaulting Cena himself and stealing the physical belt. For the next two months, Cena feuded with Khali over the championship, eventually becoming the first person in WWE to defeat him by submission at Judgment Day and then by pinfall at One Night Stand. Later that summer, Randy Orton was named the number one contender for the WWE championship, starting a feud between the two. Leading up to SummerSlam, Orton delivered a number of sneak-attacks, performing three RKOs to Cena, but in the actual match, Cena retained the championship. A rematch between the two occurred at Unforgiven, with Orton winning by disqualification after Cena ignored the referee's instructions and continued to beat on him in the corner.

During a match with Mr. Kennedy on the October 1, 2007 episode of Raw, Cena suffered a torn pectoral muscle while executing a hip toss. Though finishing the match and taking part in the scripted attack by Randy Orton after the match, surgery the following day found that his pectoralis major muscle was torn completely from the bone, estimating at the time to require seven months to a year of rehabilitation. As a result, Cena was stripped of the title in an announcement by Vince McMahon on the next night's episode of ECW, ending what was the longest WWE Championship reign in over 19 years. Cena's surgery was performed by orthopedic surgeon James Andrews at St. Vincent's Hospital in Birmingham, Alabama. Two weeks later, in a video update on WWE.com, Dr. Andrews and Cena's physical trainer both said that he was several weeks ahead of where he was expected to be in his rehabilitation at that time. Despite his injury, Cena attended the annual WWE Tribute to the Troops show filmed at Camp Speicher in Tikrit, Iraq on December 7, and aired on December 24.

Cena made an unannounced return as the final participant of the Royal Rumble match, winning the match, and the traditional WrestleMania title shot, by last eliminating Triple H. Instead of waiting until WrestleMania, the title shot was cashed in against WWE Champion Randy Orton at February's No Way Out pay-per-view in a match where Cena won by disqualification, resulting in him not getting the championship. The night after No Way Out, Cena was placed back into WrestleMania XXIV's WWE Championship match, making it a Triple Threat match also involving Triple H, during which he was pinned by Orton. At Backlash, Cena failed to regain the title in a Fatal Four-Way elimination match, in which he was pinned by Orton. Triple H won the title during that match. During the match, Cena eliminated JBL, renewing their feud from 2005. Cena defeated JBL at Judgment Day and then at One Night Stand in a First Blood match. JBL, however, defeated him in a New York City Parking Lot Brawl at The Great American Bash in July.

On the August 4 episode of Raw, Cena became a World Tag Team Champion for a second time, teaming with Batista to defeat Cody Rhodes and Ted DiBiase, but failed to retain the titles the following week against the former champions. Batista defeated Cena at SummerSlam; shortly after, he was named one of four contenders for CM Punk's World Heavyweight Championship in the Championship scramble match at Unforgiven. He was replaced by Rey Mysterio, however, after announcing Cena had suffered a herniated disc in his neck, which would require surgery. Cena underwent successful surgery to repair the injury.

Cena made his in-ring return at the November pay-per-view event, Survivor Series, defeating Chris Jericho to win his first World Heavyweight Championship. The two continued their rivalry up to Armageddon, where Cena retained his championship. Cena lost the championship at No Way Out, to Edge after Kofi Kingston was attacked by Edge, who took his place in the Elimination Chamber match. Cena was given an opportunity to regain the title at WrestleMania XXV in a Triple Threat match also involving Big Show, which Cena won.

Cena lost the championship back to Edge in a Last Man Standing match at Backlash after interference from Big Show, who chokeslammed Cena through a big spotlight. This angle resulted in Cena beginning a feud with Big Show. Cena defeated Big Show at Judgment Day and at Extreme Rules in a Submission match by applying the STF.

At the July pay-per-view, Night of Champions, he participated in a Triple Threat match for the WWE Championship, which also involved Triple H and WWE Champion Randy Orton. Cena, however, did not win the match. Two months later, at Breaking Point, Cena defeated Randy Orton for the WWE Championship in an "I Quit" match to win his fourth WWE Championship. At Hell in a Cell, Cena dropped the title to Orton in a Hell in a Cell match. Three weeks later, at WWE Bragging Rights, Cena defeated Orton in a 60-minute Iron Man match.

Two months later, Cena would lose the title to Sheamus at TLC: Tables, Ladders & Chairs in a Tables match.

In February 2010, Cena regained the WWE title at the Elimination Chamber pay-per-view in an Elimination Chamber match after last eliminating Triple H. However, immediately after the match Mr. McMahon declared that he would immediately defend his title against Batista, who had been involved with Cena in Vince McMahon and Bret Hart's rivalry. Cena lost that match to Batista, and the WWE Championship and marking one of the shortest WWE Championship reigns in history. The following night after the Elimination Chamber pay-per-view, Cena asked for a rematch for the title at WrestleMania, which McMahon gave him the opportunity to as long as he defeated Batista that night. Later that night, Batista intentionally got himself disqualified by kicking Cena in the groin to set up their match at WrestleMania XXVI. At the event, Cena defeated Batista to win back the WWE title. At the April pay-per-view, Extreme Rules, Cena defeated Batista in a rematch for the WWE title in a Last Man Standing match. He faced Batista one more time in an I Quit match at Over the Limit which he won.

On the June 7, 2010 episode of Raw, Cena was suddenly thrust into a new storyline when during his main event match against CM Punk, he was attacked by all eight former contestants of WWE NXT Season 1, with Wade Barrett as their leader. Punk, his follower Luke Gallows, and other personnel around the ring were attacked as well, but Cena took the worst of the attack and was carried out on a stretcher. This group would later refer to themselves as The Nexus.

At June's Fatal 4-Way event, Cena lost the WWE title to Sheamus in a fatal four-way match that also involved Edge and Randy Orton due to interference by Nexus. The following month, in a WWE title rematch against Sheamus in a steel cage match at the Money in the Bank pay-per-view, the group interfered, thus costing Cena the chance of regaining the championship. Cena later formed an alliance with Edge, Chris Jericho, John Morrison, R-Truth, The Great Khali and Bret Hart to face the Nexus at SummerSlam, where Cena's team defeated Nexus with the returning Daniel Bryan, a former member of Nexus, who replaced Khali after getting injured.

Nexus's actions, however, did not stop after SummerSlam. Hoping to end Nexus for good, Cena challenged Wade Barrett to a match at Hell in a Cell only to lose due to interference by two fans, later identified as Husky Harris and Michael McGillicutty. Due to the stipulations in place, Cena was forced to join Nexus. Cena had originally planned to destroy Nexus from within as a member of the group, but the Raw general manager ordered him to follow orders from Barrett, or else he would be fired. At Bragging Rights, Cena and Nexus member David Otunga defeated "Dashing" Cody Rhodes and Drew McIntyre to win the Tag Team Championship.

Later in the show Cena was forced to help Barrett to win his WWE Championship match against Randy Orton. If Barrett didn't win the match Cena would be fired. Cena twisted his words around and attacked Barrett, giving Barrett the win via disqualification but not Orton's title. The following day, Cena and Otunga lost the Tag Team Championship to fellow Nexus members Heath Slater and Justin Gabriel, when Barrett ordered Otunga to lay down and lose the title. At Survivor Series, Cena officiated a match for the WWE Championship between Wade Barrett and Randy Orton. As a part of a pre-match stipulation, if Barrett didn't win the championship, Cena would be fired from the WWE.

Orton defeated Barrett to retain the title, thus ending Cena's career in the WWE. The following day on Raw, Cena gave a farewell speech, before costing Wade Barrett the WWE Championship by interfering in his rematch with Randy Orton. A week later, Cena invaded Raw, first as a spectator, but he then attacked members of Nexus, explaining that he would still take down Nexus one by one, despite not having a job in the WWE anymore. On the December 13 episode of Raw, Cena was rehired by Barrett, in exchange that he would face him at TLC: Tables, Ladders & Chairs in a Chairs Match. Prior to TLC, Cena teamed up with Randy Orton and Rey Mysterio to defeat Wade Barrett, The Miz and Alberto Del Rio at The WWE Tribute to the Troops. On December 19 at TLC: Tables, Ladders & Chairs, John Cena was victorious against Wade Barrett in a Chairs match in the main event of the evening.

On the December 27 episode of Raw, The Nexus, minus Wade Barrett, announced they were under new management and offered to bury the hatchet with John Cena, to which Cena refused. The Nexus attacked Cena, leaving a Nexus armband in the ring during the process. As the group retreated, CM Punk, who had attacked Cena with a steel chair twice the week before, came to the ring to, what looked like attack John Cena, but instead put on the armband left behind to symbolically announce his allegiance with The Nexus. The next week, Wade Barrett returned to Raw and confronted CM Punk over the issue of who the leader of The Nexus was and who was responsible for Cena's attack the week before. Barrett was placed into a Triple Threat Steel Cage Match that night that would determine the No. 1 contender for the WWE Championship. CM Punk added his own stipulation to the match saying if Barrett lost, he would be banished from the group, but if he won he would remain leader. Wade Barrett would lose the match after CM Punk interfered by ripping of Barrett's armband.

On the January 17 episode of Raw, Cena returned and faced Punk in a match. During the match, a man, who would later be revealed to be Mason Ryan, attacked Cena. During the 2011 Royal Rumble match, Cena would eliminate most of the Nexus, ending his feud with them.

Cena competed in the 2011 Royal Rumble match at the pay-per-view, making it to the final five before being eliminated by The Miz, the current WWE Champion at the time, who wasn't an official participant in the match. At the Elimination Chamber pay-per-view, Cena won the Elimination Chamber match to face The Miz at WrestleMania XXVII for the WWE Championship. On the February 21 episode of Raw, Cena replied to The Rock's comments about him from the previous week, as The Rock returned as the announced guest host of WrestleMania, where he made a rap about Rock. That same night, Cena was placed into a WWE Tag Team Championship match, with him teaming with The Miz, where they defeated Justin Gabriel and Heath Slater to become WWE Tag Team Champions. After the match, Wade Barrett invoked Gabriel and Slater's rematch clause straight away, where they won their titles back, after Miz attacked Cena. After weeks of insults to each other, Cena met Rock face-to-face on the March 28 episode of Raw, where Cena would hit his Attitude Adjustment finishing move on Rock. At WrestleMania, Cena and Miz would fight to a double count-out, but guest host Rock would restart the match, only for him to hit his Rock Bottom finishing move on Cena, allowing Miz to retain his title. The next night on Raw, Cena and Rock agreed to face each other at WrestleMania XXVIII, making it the first match to be set up at WrestleMania one year in advance. At Extreme Rules, Cena would defeat Miz and Morrison to become WWE Champion. Cena went on to defend the title against The Miz at Over the Limit in an "I Quit" match and R-Truth at Capitol Punishment

At Money in the Bank, CM Punk defeated Cena to win the WWE Championship, and left the company with the title. A tournament was then conducted to determine the new WWE Champion for the "vacant" WWE title, which was won by Rey Mysterio on the July 25 episode of Raw. That same night, Cena challenged and defeated Mysterio to become WWE Champion for a record breaking ninth time. Following the match, CM Punk returned to the company, with the WWE Championship he won at Money in the Bank, leading to a title unification match at SummerSlam, where Punk defeated Cena to become "undisputed" WWE Champion. Punk would lose the championship following the match to Mr. Money in the Bank Alberto Del Rio. On the August 22 episode of Raw, Cena defeated Punk to become number one contender for the WWE Championship, and would defeat Del Rio at Night of Champions to become WWE Champion. Cena would then lose the title back to Del Rio two weeks later at Hell in a Cell, in a Triple Threat Hell in a Cell match also involving Punk, after Ricardo Rodriguez and Del Rio locked Cena outside of the Cell. Cena lost his rematch at Vengeance in a Last Man Standing match, due to interference by The Miz and R-Truth. After a few weeks of Miz and Truth attacking Cena and other employees, Cena was allowed to choose his partner to challenge Miz and Truth at Survivor Series. Cena would announce that he had chosen The Rock to be his partner. At the pay-per-view, after Cena and Rock defeated Miz and Truth, Rock gave Cena another Rock Bottom.

On the December 12 episode of Raw, during his match with Mark Henry, Cena was attacked by the returning Kane. The following week on Raw, Cena would call out Kane for his actions last week, but Henry would come out instead. Kane would then come out soon after, and once again attacked Cena. The following week, Kane would explain to Cena that the reason he had attacked him was in disgust of Cena's "Rise Above Hate" t-shirt slogan, stating that hate is a "natural impulse" and shouldn't be contained. He then led the fans in attendance who were not fond of Cena into chanting "Cena Sucks!" as Raw went off the air. Kane would then attack Cena's friend Zack Ryder, which led him to lose his United States Championship. At the Royal Rumble, Kane and Cena would fight each other to a double countout only for Kane to get the upper hand on Cena and Ryder, who was watching in a private room in a wheelchair, after the match. At Elimination Chamber, Cena defeated Kane in an Ambulance match to end the feud.

After Elimination Chamber, Cena and The Rock would start verbally attacking each other. At WrestleMania XXVIII, Cena faced the Rock in the main event match which had been building for a year and was billed as "once in a lifetime" and as the biggest and most important match in John Cena's career as well as the match that would determine the greatest wrestler of all time. The climax of the match came when Cena let his arrogance get in the way of victory causing him to make the mistake of attempting the People's Elbow on the Rock, as the Rock countered with a Rock Bottom to seal the victory.

The following night on Raw, Cena would address the Rock, with the crowd chanting "You're a Loser". Stating that though he lost his career's most important match, he would own up and accept not only his loss, but also the Rock being the greatest wrestler of all time. Cena would call out the Rock to congratulate him only to be interrupted by Brock Lesnar, who proceeded to hit Cena with an F5. This would result in Cena entering into a feud with Raw General Manager John Laurinaitis who was advertising Lesnar as the new face of the WWE. Laurinaitis would go on to announce Cena would face Lesnar at the main event of Extreme Rules. Cena would be confronted by Edge who would acknowledge Cena's loss to the Rock causing him to have a lack of focus. Edge would go on to tell Cena to wake up from his loss to the Rock and beat Brock Lesnar to stop Laurinaitis for promoting a superstar who doesn't care for the WWE. Later that night, Cena showed his lack of confidence by bringing a chain to the contract signing and refusing to fight Lesnar. At the event, Cena would end up winning after hitting Lesnar with the Attitude Adjustment. On the following Raw, Cena would be confronted by Laurinaitis, Cena would claim for the GM to have hired Lesnar as a mercenary to take him out, prompting Laurinaitis to attack Cena and declare himself as Cena's opponent at Over the Limit. Cena would go on to lose the match against Lauranitis. It would then further be announced by Laurinaitis that Cena would be facing the Big Show at No Way Out with the stipulation that dependent on the victor of the match, either Cena or Laurinaitis would be fired. Cena would go on to win the match against Big Show and proceed to do the Attitude Adjustment on Laurinaitis through the announce table, while Vince McMahon would go on to say "You're Fired" to Laurinaitis. Cena would continue to feud with the Big Show and would subsequently enter the Money in the Bank Ladder Match at the Money in the Bank Pay-Per View to try and the stop the Big Show from winning. At Money in the bank, Cena would go on to win the Money In The Bank match, acquring himself a contract which he could cash in at any time of his choosing for a WWE Championship match for up to a year.

On July 23 at Raw 1000, Cena cashed in his Money in the Bank contract on CM Punk; Cena won the match by disqualification after interference from Big Show, thus becoming the first person to ever cash in a Money in the Bank contract and not win a title. Show would continue to attack Cena until the Rock arrived to make the save. The following week on Raw, a WWE Championship number one contenders match between Cena and Show ended in a no contest due to interference from Punk. Following this, both men were entered in the championship match at SummerSlam by Raw General Manager AJ. At the event, however, Cena would be unsuccessful in winning the championship as Punk would go on to retain the title once more. Over the next few weeks, Cena would continue to feud with Punk by refusing to call him best in the world and fighting him to a draw at Night of Champions. On September 20, Cena would be put out of action for six to eight weeks due to an arm injury, but would still attempt to compete for the WWE Championship. However, on the October 15 episode of Raw, Cena opted out of a possible match at Hell in a Cell and instead thrusted Ryback into the title picture. On the November 5 episode of Raw, Cena, along with Ryback, would be booked in a triple threat match for Punk's WWE Championship at Survivor Series while starting to feud with Dolph Ziggler over the topic of AJ Lee. However, at Survivor Series, Punk would once again pin Cena to retain the championship. On the December 3, 2012 episode of Raw, Cena was put into a match at TLC against Ziggler by Vickie Guerrero, with Ziggler's World Heavyweight Championship Money in the Bank contract on the line. On December 16 at TLC: Tables, Ladders & Chairs faced Ziggler in a ladder match for his World Heavyweight Championship Money in the Bank contract on the line, but lost after AJ turned on Cena. The following night on Raw, Cena teamed with Vickie Guerrero to face Ziggler and AJ in a mixed tag team match, however, the match ended in a disqualification after Cena was attacked by the debuting Big E Langston. Cena then defeated Ziggler on the January 7, 2013, episode of Raw in a singles match, and again in a steel cage match the following week, despite interference from AJ an Langston in both matches.

On January 27 at the Royal Rumble, Cena entered the Rumble at #19 and won the match after last eliminating Ryback, becoming the fourth wrestler (after Hulk Hogan, Shawn Michaels and Stone Cold Steve Austin) to win multiple Rumble matches. The following night on Raw, Cena announced that he would pursue the WWE Championship at Wrestlemania 29, after which, he would be assaulted by The Shield. The following week on Raw, Cena would gain vengeance on the Shield when he, along with Ryback and Sheamus, attacked the stable. This culminated in a six-man tag team match on February 17 at Elimination Chamber, where the Shield emerged victorious. On the February 25 episode of Raw, Cena defeated CM Punk to reaffirm his status as number one contender for the Rock's WWE Championship. Cena then returned to his rivalry with The Rock, with Cena claiming that he had to defeat Rock to get redemption for his professional and personal troubles. On April 7 at Wrestlemania 29, Cena defeated Rock to win his eleventh WWE Championship. The following night on Raw, Cena began a rivalry with Ryback, after he saved Cena from a post-match assault from Mark Henry only to attack Cena himself. At the same time as his feud with Ryback, Cena would suffer a legitimate achilles tendon injury, while also battling the Shield and facing them in losing efforts. On May 19 at Extreme Rules, Cena retained the WWE Championship against Ryback in a Last Man Standing Match after Ryback rammed Cena and himself into the electric backdrop at the top of the ramp, resulting in a no contest. On June 16 at WWE Payback, Cena defeated Ryback in a 3 Stages of Hell match to retain the WWE Championship, with Cena losing the Lumberjack match and winning the Tables match and the Ambulance match. The following night on Raw, Cena was attacked by the returning Mark Henry, who feigned his "retirement", with a World's Strongest Slam, sparking a rivalry between the two. On July 14 at Money in the Bank, Cena defeated Henry via submission to retain the WWE Championship. The next night on Raw, new Raw general manager Brad Maddox announced that he would allow Cena to choose his own opponent for SummerSlam. Later in the night, after taking an informal poll of the live audience, he chose Daniel Bryan. On August 18 at the pay-per-view, Cena lost the WWE Championship to Bryan, with Triple H as the special guest referee, ending his reign at 133 days. The following night on Raw, Cena announced that he would undergo surgery for a triceps tear and would be out for 4 to 6 months.

On the October 7th edition of Raw, it was announced that John Cena would be returning at Hell in a Cell. There, he defeated Alberto Del Rio for the World Heavyweight Championship. The following day on Raw John Cena defeated Damien Sandow in his first title defense for his current reign. On November 8 episode of SmackDown Cena confronted Del Rio in the ring who was complaining that he was sick in their Hell in a Cell match, and challenged him to a rematch at, but was it would have to be put on hold has the SmackDown General Manager Vickie Guerrero made it clear that they would face eachother at Survivor Series on November 24. Cena successfully defended the World Heavyweight Championship against Del Rio at Survivor Series. On the November 25 edition of Raw, John Cena suggested that there only be "one champion" in WWE, so Triple H stated there would be a unification match between him and Randy Orton at TLC. Cena went on to lose the match to Orton, losing the World Heavyweight Championship in the process. Stephanie McMahon announced a rematch, in which Orton would defend the WWE World Heavyweight title against Cena at the Royal Rumble. Orton defeated Cena at the Rumble following a distraction by The Wyatt Family. Cena was then attacked after the match by the Wyatts. The following night on Raw, Cena teamed up with Sheamus and Bryan to defeat The Shield via disqualification by the Wyatt Family and was qualified to compete in an Elimination Chamber match for the WWE World Heavyweight Championship at Elimination Chamber 2014. At Elimination Chamber, the Wyatts cost Cena the match once again which led to Orton pinning him for elimination. The next night on Raw, Cena would respond by calling out the Wyatts, which led to a vicious attack injuring Cena. On the March 10 edition of Raw, Cena announced his intention to participate in the André The Giant Memorial Battle Royal, but after Wyatt accused Cena and Hulk Hogan of being "liars", insinuating their heroic personas were just facades, Cena instead issued a challenge to Wyatt for the PPV, which Wyatt later accepted. At the event, Cena maintained his legacy and defeated Wyatt. Cena afterwards then called Wyatt out for not being able to defend his cryptic speeches without Luke Harper and Eric Rowan behind him. To make Wyatt prove himself, Cena challenged him a steel cage match at Extreme Rules, which Wyatt accepted. At the event, John Cena, after fending off all three Wyatts, preceded to walk out of the cage door, but was stopped by the lights going out, and a little kid named "Little Johnny" singing "He's Got The Whole World In His Hands" in a distorted voice. Wyatt then applied Sister Abigail and walked out victorious. Cena's feud with Wyatt continued with a Last Man Standing match being set up for Payback. At the pay-per-view, Cena buried Wyatt under multiple equipment cases to win the match.

The next night on Raw, Cena faced Kane after interrupting Stephanie McMahon, who was criticizing Daniel Bryan's decision not to vacate the WWE World Heavyweight Championship at the Payback pay-per-view. McMahon revealed an ultimatum for the champion; be fit for the Money in the Bank pay-per-view or the title will be held for the first time in Money in the Bank ladder match. Cena went on to call McMahon a spoiled, jealous, ego maniac. Stephanie, in return, set Cena up against Kane. Cena won via disqualification, and was subject to being thrown into the steel steps. Cena retaliated, and threw the steps at Kane. The following week, after remaining Shield members Dean Ambrose and Roman Reigns  addressed Seth Rollins, they were attacked by The Wyatt Family. Cena came to their aid and was added in The Shield's six man tag team match against the Wyatts, which resulted in The Shield and Cena winning.

On the June 16 edition of Raw, Cena was forbidden by The Authority to participate in a battle royal for a spot in the Money in the Bank ladder for the vacant WWE World Heavyweight Championship, but he would instead earn a spot another way: facing Kane in the originally proposed Stretcher match Daniel Bryan was supposed to fight. During the match, Cena delivered an AA to Kane through the announcer's table, but was attacked by Rollins and Randy Orton as he tried to carry Kane up the ramp. Rollins and Orton, in turn, were attacked and fended off by Ambrose, and Cena hit another AA to a revived Kane onto the stretcher, allowing him to push Kane over the line and earn his spot for the main event at Money in the Bank. At the pay-per-view, he captured his 15th world championship by winning the WWE World Heavyweight Championship in the main event. Cena then retained the title at Battleground against Roman Reigns, Randy Orton and Kane. At SummerSlam, Cena lost the championship to Brock Lesnar in a squash match, during which Lesnar hit Cena with sixteen German Suplexes and two F-5s. It was announced later in the week on Main Event that Cena would invoke his rematch clause at Night of Champions, in which Cena won via disqualification after Seth Rollins got involved. Cena then began feuding with Dean Ambrose for the right to face Rollins at Hell in a Cell, but Ambrose got that right after beating Cena in a No Holds Barred Contract on a Pole match, after which they shook hands in respect. Cena would instead face Randy Orton in a Hell in a Cell match to determine the number one contender to face Lesnar for the World Title, which Cena won by sending Orton into a table with an AA from the top turnbuckle.

On October 27 episode of Raw, Cena rejected the Authority's offer to join forces. This resulted in a 5-on-5 Survivor Series elimination tag match between Team Cena and Team Authority at Survivor Series 2014. At Survivor Series, one of Cena's team-mates, Big Show, turned on and attacked him, causing Cena's elimination, but Dolph Ziggler eventually won the match for Team Cena with the interfering Sting's help. Thus as per the match stipulation, the Authority were stripped from power and only Cena could bring them back. At the TLC pay-per-view, Cena defeated Rollins, thus keeping his WWE title shot. On the December 29 episode of Raw, Seth Rollins and Big Show held guest host Edge hostage, forcing Cena to reinstate the Authority. Even so, Rollins tried to break Edge's neck anyway, but was thwarted by Cena. On 19 January edition of Raw, Cena won a handicap match against Seth Rollins, Big Show and Kane. This meant that Dolph Ziggler, Ryback and Erick Rowan could get their jobs back because they were fired a couple of weeks before. At Royal Rumble 2015, Cena was unsuccessful to capture the WWE World Heavyweight Championship in a triple threat match where Brock Lesnar pinned Seth Rollins.

Following the Royal Rumble, Cena began feuding with the United States Champion Rusev. At Fastlane, Rusev defeated Cena by making him pass out to remain the United States Champion. This was Cena's first pass out loss in his career. In the following weeks, Cena challenged Rusev to a rematch, which was declined. Stephanie McMahon decreed that Cena would not compete at WrestleMania unless Rusev agreed to a match. On the March 9 episode of Raw, Cena attacked Rusev, refusing to release the STF submission hold even though Rusev tapped out. This continued until Lana granted Cena a title rematch at WrestleMania against Rusev. At the event, Cena pinned Rusev to win the United States Championship for the fourth time and ended Rusev's undefeated streak since coming to the main roster. The following night on RAW Cena made an Open Challenge to any superstar to challenge him for the title, which was answered by Dean Ambrose, however Cena defeated Ambrose to retain his title, and also Cena defeated for the title Stardust the following week on RAW in another Open Challenge. On the April 2 episode of SmackDown, Rusev would challenge Cena to a rematch for the title at Extreme Rules, which Cena accepted. It was announced that their match would be a Russian Chain Match. In the following weeks leading up to Extreme Rules, Cena would retain the title in his Open Challenges to Bad News Barrett and Kane. Cena defeated Rusev at the event to retain the title, but it was later announced that Cena would once again defend the title against Rusev in an "I Quit" match at Payback, which Cena controversially won when Lana told the referee Rusev said he quit in Bulgarian; the ring announcer had said the loser must "literally say the words 'I quit'". Leading up to Payback, Cena defeated the likes of NXT superstar Sami Zayn and Neville. On the Raw after Payback, Cena was attacked by NXT Champion Kevin Owens, setting up a match between Cena and Owens at Elimination Chamber. Owens defeated Cena, but a rematch was then scheduled for Money in the Bank, which Cena won. Owens then challenged Cena to a match for the United States Championship at Battleground, which Cena accepted. Cena then defeated Owens at Battleground to retain the United States Championship.

On the July 20 episode of Raw, Cena issued a challenge to Seth Rollins for the WWE World Heavyweight Championship, which Rollins refused. The following week, Cena again issued a challenge to Rollins for the title, with The Authority this time refusing the match, instead making Cena defend his United States Championship against Rollins. Later that night, Cena retained his title against Rollins, suffering a legitimate broken nose during the match. On the August 3 episode of Raw, Rollins challenged Cena to a "Winner Takes All" match at SummerSlam, for both the WWE World Heavyweight Championship and the United States Championship. On the August 11 episode of Tough Enough, Cena accepted Rollins' challenge. Rollins defeated Cena after guest host Jon Stewart, appearing to side with Cena, instead attacked Cena with a steel chair, ending Cena's reign as United States Champion at 147 days. On the August 31 edition of Raw, Cena invoked his rematch clause to face Rollins for the WWE United States Championship at Night of Champions, where he defeated Rollins to win the title for the record fifth time in WWE. On the following Raw, Cena retained his title against Seth Rollins in a rematch set by Corporate Kane. At Hell in a Cell, Cena lost the title to Alberto Del Rio in an open challenge. Following Hell in a Cell, Cena announced he was taking time off. It was announced on December 21 episode of Raw that Cena would return to face Alberto Del Rio for US title on following episode of Raw. At the event, he was unsuccessful.

On January 7, it was announced that Cena sustained a shoulder injury, with recovery time slated around 6-9 months. Cena returned at WrestleMania 32 on April 3, helping former rival The Rock fend off The Wyatt Family. After the event it was reported that Cena had not yet been cleared to return to full-time competition and would be on the sidelines for at least one more month.

On April 25, 2016, Cena announced on Twitter that he will return on the May 30 (Memorial Day) edition of Raw, four months earlier than had been expected for his type of injury. Cena then made his full return on the May 30 edition of Raw, four months earlier than had been expected for his type of injury. He was confronted by AJ Styles, only to be betrayed by Styles, who joined his former Club teammates Luke Gallows and Karl Anderson in attacking Cena. This set up a match between Cena and Styles at Money in the Bank, which Styles won with interference from Gallows and Anderson. On the July 4 episode of Raw, Cena was again attacked by the Club, but was saved by Enzo Amore and Big Cass. Subsequently, a six-man tag team match was made between the two teams for Battleground. On July 19 at the 2016 WWE draft, Cena was drafted to SmackDown. Cena, Amore and Cass defeated The Club at Battleground after Cena pinned Styles. Styles then challenged Cena to another match at SummerSlam, which Cena accepted. Styles then defeated Cena at SummerSlam, after which Cena took off his wristband and left it in the ring. After his brief hiatus from television, Cena returned on September 13, where it was announced that he would face Dean Ambrose and newly crowned champion AJ Styles for the renamed WWE World Championship at No Mercy. On the same episode, Cena would team with Ambrose in a winning effort against Styles & The Miz. Cena lost the match at No Mercy after being pinned by Styles, which came after Ambrose and Cena simultaneously made Styles submit, therefore restarting the match. On the December 13 episode of SmackDown Live, it was announced that Cena would be returning on the December 27 episode. On his return, he addressed rumors about him during the past year, stated that the New Era was "B.S.", and then challenged the winner of that night's championship match, which was AJ Styles, for the again renamed WWE Championship at the Royal Rumble. The next week on SmackDown, Cena and Styles took part in a contract signing for their match at the Rumble.