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In 2002, Bryan came to World Wrestling Entertainment to compete on its secondary programming, Velocity and Heat, initially as enhancement talent before being allowed to compete in longer matches; he once wrestled future WWE Champion John Cena in a losing effort.

Bryan made his debut as a WWE contracted wrestler on January 4, 2010, in a dark match prior to Raw, defeating Chavo Guerrero.

On February 16, it was announced that he would wrestle on the first season of the NXT show with The Miz as his storyline mentor. He made his debut on the inaugural episode of NXT on February 23, losing by submission to the World Heavyweight Champion, Chris Jericho. After the match, Bryan was attacked by The Miz for disrespecting him earlier in the show. Over the next several weeks, Bryan failed to win a single match, but despite having a win-loss record of 0–5, he was ranked first in the inaugural Pros' Poll on the March 30 episode of NXT. After losing five more matches on NXT, Bryan earned his first victory on the May 10 episode of Raw by pinning Santino Marella in an eight-on-four handicap match. The following night on NXT, he was eliminated from the show, along with Michael Tarver, as neither man had confidence in themselves to win the competition. Despite his elimination, he appeared on the following episodes of NXT, being interviewed by Matt Striker and attacking both Michael Cole, who had constantly belittled him on commentary, and The Miz.

On the May 31 episode of Raw, Bryan defeated The Miz in a singles match, and after the match, he threw The Miz into Cole, who was commentating at ringside. The following week on Raw, the season one NXT rookies interfered in the main event match between John Cena and CM Punk, attacking both competitors, the announce team, and the ring announcer Justin Roberts, before dismantling the ring area and surrounding equipment, turning Bryan and the other rookies heel in the process. On June 11, 2010, WWE announced that Bryan was fired from WWE. His release was put in a storyline, where the rest of the NXT rookies kicked him out of the group for showing remorse for his actions and declared that Bryan will never return to the WWE again.

On August 15, 2010, Bryan returned to WWE at the SummerSlam pay-per-view, where he was revealed as the surprise seventh member of Team WWE for the seven-on-seven elimination tag team match against The Nexus, the other NXT season one competitors. At the event, Bryan was one of the two final members of Team WWE, and managed to eliminate two members of the Nexus, but was eliminated by Wade Barrett after his former pro The Miz, whose place he took in Team WWE, attacked him. Despite this, Team WWE won the match. The following night, he was revealed as part of the Raw roster. He feuded with the Miz, with both interfering in each other's matches, and The Miz being aided by Alex Riley, his rookie from the second season of NXT. At Night of Champions, Bryan defeated The Miz to win the WWE United States Championship, his first championship in WWE.

He then successfully defended the championship two weeks later, by defeating The Miz and John Morrison in a triple threat submissions count anywhere match at Hell in a Cell. Bryan went on to challenge then Intercontinental Champion Dolph Ziggler to a Champion vs. Champion match at Bragging Rights as a special attraction Smackdown vs. RAW match, defeating Ziggler in a highly acclaimed match. Bryan went on to successfully defend his United States tite against Ted DiBiase at Survivor Series. On the November 30 episode of NXT, it was announced that Bryan was returning to the show as the Pro to NXT Rookie Derrick Bateman on season four. In late 2010, The Bella Twins began competing for Bryan's affection, leading to them supporting him at ringside and competing in mixed tag team matches together. On the January 24, 2011 episode of Raw, it was revealed that Bryan had been secretly dating Gail Kim, who began accompanying him to ringside. On the March 14 episode of Raw, Bryan lost the United States Championship to Sheamus. Bryan was originally scheduled to have his rematch against Sheamus for the United States Championship on the main card at WrestleMania XXVII, but the match was rescheduled as a preshow dark match; a lumberjack match that ended in a no contest when the lumberjacks fought among themselves to trigger the start of a battle royal. Bryan lost his title rematch the next night on Raw, after which he was saved from Sheamus by the debuting Sin Cara.

On April 26, Bryan was drafted to the SmackDown brand as part of the 2011 Supplemental Draft. Bryan debuted for the SmackDown brand on the May 6 episode, when he lost to Sheamus. Cody Rhodes then started a feud with Bryan by attacking him after losing their match and placing a paper bag on his head. Bryan then aligned with Sin Cara to feud with Cody Rhodes and Ted DiBiase. On June 28, Bryan returned to NXT to manage Derrick Bateman once again.

On July 17 at Money in the Bank, Bryan won the SmackDown Money in the Bank ladder match which earned him a World Heavyweight Championship at any point within the following year. On the July 22 episode of SmackDown, Bryan declared he would cash in his Money in the Bank briefcase at WrestleMania XXVIII. After several months of losing matches, Bryan began a feud with World Heavyweight Champion Mark Henry on the November 4 episode of SmackDown, after Henry challenged Bryan to a non-title match to prove that Bryan could not become champion. During the match, Big Show knocked out Henry, making him win by disqualification. Big Show, as a friend of Bryan, then urged a groggy Bryan to cash in his championship match, but Henry recovered and attacked both Bryan and Big Show before the match could start. After losing a rematch, Bryan suffered attacks from Henry the following two weeks. On November 25, Henry was knocked out again by Big Show, at which point Bryan cashed in his briefcase for a title match and quickly pinned Henry. However, SmackDown authority figure Theodore Long revealed that Henry was not medically cleared to compete and voided the match, so Henry remained champion and the briefcase was returned to Bryan. Bryan later admitted he betrayed his principles by not waiting for WrestleMania, but explained he felt strongly about exacting revenge on Henry and realised he may not make it to WrestleMania due to Henry's continued attacks. Regardless of his briefcase, Bryan won a four-way match on the same episode of SmackDown to become the contender for Henry's championship. On the live November 29 SmackDown, Henry managed to pin Bryan to retain his title in a steel cage match. Also in November, Bryan started being involved in a romantic storyline with AJ.

Bryan cashed in his Money in the Bank contract on December 18 at TLC: Tables, Ladders & Chairs against Big Show, who had just defeated Henry and subsequently received a DDT onto a steel chair, which allowed Bryan to secure a pinfall victory and become the World Heavyweight Champion. In the following weeks, tension was teased between Bryan and Big Show, with Big Show unhappy about Bryan taking the world championship from him, and Bryan being displeased about Big Show's lack of appreciation for Bryan's help in matches against Henry. As World Champion, Bryan began a slow heel turn as he gradually showed signs of overconfidence and arrogance, with Bryan beginning to partake in excessive victory celebrations, even when he won his matches by disqualification or count-out. Also, despite AJ's declaration of love for Bryan, Bryan avoided saying that he loved her in return.

In January 2012, Bryan successfully defended his title thrice; the first occasion against Big Show when Bryan goaded Mark Henry into attacking him and causing a disqualification; the second occasion a No Disqualification rematch with Show which ended abruptly after Show accidentally ran into AJ, hospitalizing her within the storyline for which Bryan blamed him; the third occasion against Henry in a Lumberjack match when Bryan provoked the lumberjacks to interfere and cause a no contest. This culminated in a Triple Threat Steel Cage match to exclude outside interference; at the 2012 Royal Rumble event, Bryan escaped the cage after freeing himself from Big Show's grasp to retain his championship.

At Elimination Chamber, Bryan defeated Big Show, Cody Rhodes, The Great Khali, Santino Marella, and Wade Barrett in an Elimination Chamber match to retain the World Heavyweight Championship. After the match, Sheamus attacked Bryan and chose him as his WrestleMania opponent for the World Heavyweight Championship. In March, Bryan began to mistreat AJ, publicly demanding her to shut up and claiming that she always got in his way. Despite these actions, AJ continued to stand by Bryan. Bryan's reign as world champion ended when Sheamus defeated him in eighteen seconds at WrestleMania XXVIII due to Bryan being distracted with receiving a good luck kiss from AJ. On the next episode of SmackDown, Bryan blamed AJ for his world title loss and ended their relationship. Despite AJ's attempts to mend their relationship, Bryan cruelly rebuffed her multiple times, leaving AJ an emotional wreck. At Extreme Rules, Bryan failed to regain the World Heavyweight Championship from Sheamus in a 2-out-of-3 falls match, losing two falls to one.

The following night on Raw, Bryan became the number one contender to CM Punk's WWE Championship when he won the Beat The Clock challenge by defeating Jerry "The King" Lawler in under 3 minutes. Bryan received his title shot at Over the Limit; he suffered a controversial loss when Bryan rolled back onto his shoulders as he applied the Yes Lock on Punk, Punk tapped out immediately after the referee counted a pinfall win for Punk. Shortly before Over the Limit, Bryan interfered in a match between Punk and Kane to frame Punk attacking Kane with a steel chair, leading to a three-way feud. During this time, a jilted AJ turned her affections to both Punk and Kane. On the June 1 episode of SmackDown, Bryan's interference caused WWE Championship match between Punk and Kane to end in a double disqualification, resulting in a triple threat match being set up at No Way Out, where Punk managed to retain the title after AJ distracted Kane. On the June 25 episode of Raw, Bryan defeated Punk and Kane in a non-title three-way elimination match to earn another shot at the WWE Championship. At Money in the Bank, Bryan failed again to capture the WWE Championship from Punk in a No Disqualification match with AJ as special guest referee. The following night on Raw, AJ accepted Bryan's marriage proposal. The following week on Raw 1000, Bryan's wedding ended in failure when AJ left Bryan at the altar and instead accepted Mr. McMahon's offer of the position of permanent Raw General Manager. Bryan's night turned from bad to worse as he was later attacked by The Rock and insulted by celebrity Charlie Sheen.

AJ's rejection of Bryan turned him into an angry and bitter individual and resulted in Bryan lashing out at audiences. AJ continued to exact her revenge on Bryan by denying him a WWE Championship shot and instead forcing him to face Kane at SummerSlam, where Bryan emerged victorious. As a result of Bryan and Kane's issues, AJ enrolled them in anger management classes hosted by Dr. Shelby. They were later forced to "hug it out". At the arrangement of Dr. Shelby and AJ, the two adversaries formed a team whose constant bickering and infighting even during matches inadvertently resulted in them defeating the Prime Time Players (Titus O'Neil and Darren Young) to become the number one contenders to the WWE Tag Team Championship on the September 10 episode of Raw and then defeating champions Kofi Kingston and R-Truth to win the Tag Team Championship at Night of Champions. Bryan and Kane made their first successful title defense the following night on Raw, defeating the former champions in a rematch. The following week on Raw, "Team Hell No" was chosen as the official team name via a Twitter poll while Team Rhodes Scholars (Cody Rhodes and Damien Sandow) started a feud with Bryan and Kane. On October 28 at Hell in a Cell, Team Hell No lost to the Rhodes Scholars via disqualification, but retained their title. Team Hell No made another successful title defense on the November 14 of Main Event by defeating the Rhodes Scholars in a rematch. On the November 26 episode of Raw, after Kane lost to WWE Champion CM Punk in a non-title match, both Bryan and Ryback, who had attempted to save Kane, were assaulted by The Shield (Dean Ambrose, Seth Rollins and Roman Reigns). This attack had the effect of uniting Bryan and Kane, and after The Shield and Team Hell No, along with Ryback, attacked each other on the December 3 episode of Raw, all six men were decreed to face each other in a Tables, Ladders, and Chairs match at TLC: Tables, Ladders & Chairs, where The Shield was victorious. On the following episode of Main Event, Team Hell No defeated Team Rhodes Scholars to retain the WWE Tag Team Championship. On the December 31 episode of Raw, Team Hell No successfully defended their titles against 3MB (Drew McIntyre and Heath Slater). Bryan ended 2012 having wrestled the second most TV/PPV matches that year with 90. On January 27 at the 2013 Royal Rumble pay-per-view, Team Hell No retained the WWE Tag Team Championship against Team Rhodes Scholars. Later that night, after Bryan eliminated Kane from the Royal Rumble Match, Antonio Cesaro threw Bryan out of the ring immediately. Kane caught Bryan before he hit the floor and despite Bryan's begging refused to put him back into the ring. On the February 4 episode of Raw, Bryan was inserted into the World Heavyweight Championship #1 contender Elimination Chamber match after he defeated Rey Mysterio, after which, the returning Mark Henry attacked both men. On February 17 at Elimination Chamber, Bryan was the first man eliminated from the match, courtesy of Henry. Over the next month, leading up to WrestleMania 29, Bryan and Kane had various matches, together and apart. During that time, they were challenged by Dolph Ziggler and Big E. Langston for the WWE Tag Team Championships at WrestleMania 29 where the team (Bryan and Kane) emerged victorious. Team Hell No rekindled their rivalry with The Shield the following night on Raw, after saving The Undertaker from an attack by the The Shield. On the April 22 episode of Raw, Team Hell No and The Undertaker were defeated by the Shield in a six-man tag team match. On May 19 at Extreme Rules, Bryan and Kane lost the WWE Tag Team Championship to Shield members Seth Rollins and Roman Reigns, ending their reign at 245 days.

As Bryan being pinned led to the loss of the tag titles, Bryan entered into a storyline in which he became obsessed about proving that he was not the weak link of Team Hell No and needing respect from others. As a result, Bryan became even more aggressive, but his overzealous behavior led to Team Hell No losing their rematch against Reigns and Rollins on the May 27 episode of Raw. Despite Kane's reassurances, Bryan had only harsh rebukes for Kane which eventually alienated Kane from him. On the June 14 episode of SmackDown, Bryan ended the Shield's unpinned/unsubmitted streak in televised six-man tag matches by submitting Rollins in a match with Kane and Randy Orton as his tag partners. Three days later at WWE Payback, Bryan and Orton unsuccessfully challenged Reigns and Rollins for the WWE Tag Team Championship. The following night on Raw, while the status of Team Hell No was left up in the air after both members considered individual pursuits, Bryan and Orton faced off in a No Disqualification match, that Orton won via referee stoppage after Bryan suffered a legitimate nerve injury. Four days later on SmackDown, Bryan defeated Orton, but to Bryan's dismay, it was via count-out. On the next episode of Raw, Bryan decisively defeated Orton via submission in a Street Fight. On July 14 at Money in the Bank, Bryan competed in the WWE Championship Money in the Bank ladder match, but was unsuccessful as the match was won by Orton. The next night on Monday Night Raw, John Cena picked Daniel Bryan out of the entire WWE lineup to be his challenger at SummerSlam 2013. On the July 22 episode of Raw, Bryan ran a guantlet match to prove his worth as #1 contender. He defeated Jack Swagger and then Antonio Cesaro, but his third opponent, Ryback was disqualified after powerbombing Bryan through a table. The next Raw, Bryan was forced to face Kane and emerged victorious, but Kane attacked him after the match. On August 18 at SummerSlam, Bryan pinned Cena to win his first WWE Championship. Immediately following the match, special referee Triple H attacked Bryan, leading to Randy Orton cashing in his Money in the Bank contract to pin Bryan and win the title. The next night on Raw, Bryan started a feud with Vince McMahon, Triple H and Stephanie McMahon, who had labelled Bryan a "B-plus," not the type of "Face of WWE" that the company is looking for as champion, instead of the "A-plus" Orton.

With Triple H threatening to fire anyone who disobeyed him, Bryan was left alone to take on and suffer attacks from Orton and the Shield. At Night of Champions 2013, Daniel Bryan defeated Randy Orton to win his second WWE championship, but was stripped of the title the next night on Raw by Triple H after referee Scott Armstrong admitted he had made a fast-count the previous night resulting in Bryan's win, while Bryan denied that Armstrong was working for him. Bryan and Orton faced off again for the vacant title on October 6 at WWE Battleground, but the match ended in a no contest after Big Show interfered and knocked out both men. At Hell in a Cell, Bryan would lose the WWE title match to Randy Orton after the special guest referee Shawn Michaels superkicked Bryan after Bryan attacked Shawn's best friend Triple H. Bryan was then attacked by the Wyatt Family just after confronting his former mentor on the next episode of Monday Night Raw, with Bray quoting that "the Devil made me do it".

He then formed an alliance with former rival CM Punk, after both began being targeted by them. On November 18 Raw, Rey Mysterio returned and helped them overcome the Wyatts and the Real Americans. As a result, Bryan allied himself with CM Punk, and the duo defeated Luke Harper and Erick Rowan of the Wyatt Family at Survivor Series, but the entire Wyatt Family defeated Bryan in a handicap match at TLC: Tables, Ladders & Chairs, with Wyatt attempting to recruit Bryan in the previous weeks. On the final Raw of 2013, Bryan defeated Harper and then Rowan in a gauntlet match so that he could face Wyatt, whereupon Harper and Rowan interfered for a disqualification and beat him down. Bryan then acknowledged that no matter how many times the fans chanted "Yes!" or supported him, it wasn't enough for "the machine", so he gave up and decided to join the Wyatt Family (briefly wrestling under the ring name "Daniel Wyatt" at house shows). On the January 13 Raw, after the Wyatt Family punished him for their lack of success since he joined, Bryan attacked all the other members of the Wyatt Family to break free from the group. At the Royal Rumble pay-per-view event, Wyatt defeated Bryan in a singles match, but the fans were extremely vocal in support of Bryan, chanting his name in the WWE World Heavyweight Championship match between John Cena and Randy Orton and the Royal Rumble match itself. The next night on Raw, he discussed this with The Authority and decided to have him team with Cena and the recently returning Sheamus to face the Shield with the winning team gaining spots for the Elimination Chamber Match and was successful.

Meanwhile, he also continued his feud with the Authority, as Kane attacked him on multiple occasions, attempting to injure Bryan before his Elimination Chamber match. At the Elimination Chamber event, Bryan survived until he was one of the final two participants in the Elimination Chamber match, but defending champion Randy Orton retained after Kane interfered against Bryan. On the March 10 Raw, Bryan and multiple fans occupied the ring and refused to leave, resulting in an irate Triple H agreeing to Bryan's demand for a match at WrestleMania XXX with the stipulation that if Bryan won, he would be inserted into the WWE World Heavyweight Championship match at the event. At Wrestlemania, Daniel Bryan defeated Triple H, and was inserted into the title match. He went into the main event with a badly injured shoulder but defeated Randy Orton and Batista to win the WWE World Heavyweight Championship by making Batista submit. After successfully defending the championship against Triple H in a one on one match, Bryan resumed feuding with his former partner, Kane. After getting married to Brie and learning Kane was his next challenger, Kane brutally assaulted Bryan in front of Brie by executing a Tombstone Piledriver three times outside the ring on the floor, on the steel steps and lastly on the announcing table, despite Stephanie McMahon's orders. He was taken away on a stretcher afterwards. In real life, Bryan's father had recently passed away, so this angle was put in place to give Bryan time off. Bryan would then go on to defeat Kane at Extreme Rules to retain his title.

On the May 12 episode of Raw, Bryan announced that he would undergo neck surgery, and would be absent from WWE for an unspecified amount of time. That same night, Stephanie McMahon called Bryan to the ring, before Kane dragged him out into the entrance before being loaded onto a stretcher by medical personnel. On May 15, Bryan underwent successful neck surgery, with a cervical foraminotomy to decompress the nerve root having been performed. Bryan returned on the May 26 episode of Raw, where he refused to relinquish his title. Stephanie McMahon threatened to fire Bryan's wife Brie Bella if Bryan did not give up his championship at Payback. At Payback, Brie Bella quit the WWE, causing Bryan to not have to give up the title. The next night on Raw, Stephanie McMahon announced that at Money in the Bank - if Bryan were able to compete - it would be against Kane in a Stretcher match, otherwise he would be stripped of the WWE World Heavyweight title. On the June 9 episode of Raw, The Authority announced that due to Bryan's neck injury, he was stripped of the title effective immediately and the vacant title would be on the line at the Money in the Bank pay-per-view.

Bryan returned to WWE television on the November 24 episode of Raw, taunting the recently deposed Authority. Bryan was instated as the Guest General Manager for that episode of Raw and the next episode of SmackDown for November 28, so he arranged for the punishments of those allied with the Authority. Apart from announcing a Chairs match between Kane and Ryback for TLC, Bryan also responded with "Yes!" to a question on whether he would return soon.

On the December 29 episode of Raw, Bryan declared that he will be able to continue his career and would be participating in the 2015 Royal Rumble match. Bryan would make his in-ring return against Kane on the January 15, 2015 episode of SmackDown, where he won by disqualification after the interference from Seth Rollins and Big Show. Following this in the same night, he teamed up with Roman Reigns and Dean Ambrose to compete against Rollins, Show and Kane which they won. After the match, Triple H announced Daniel Bryan would face Kane in a rematch on January 22 with his Royal Rumble spot on the line. On the January 22, 2015 episode of SmackDown, Daniel Bryan defeated Kane in a No Disqualification match to keep his Royal Rumble match spot.

Bryan entered the 2015 Royal Rumble match at number 10, managing one elimination, before being eliminated by Bray Wyatt in the first-half of the match. This caused the Philadelphia crowd to repeatedly chant for him during the second-half of the match, while booing other wrestlers entering the match, including eventual winner and usual fan favourite Roman Reigns.

On the January 29 episode of SmackDown, Bryan ended his feud with Kane by defeating him in a casket match. On the February 2 episode of Raw, Bryan defeated Seth Rollins, thus earning the right to face Roman Reigns at WWE Fastlane; the winner of the Fastlane match would challenge Brock Lesnar at WrestleMania 31 for the WWE World Heavyweight Championship. At Fastlane, Bryan lost to Reigns, failing to make his entry to WrestleMania main event.

Post-Fastlane, Bryan became involved in the Intercontinental Championship picture for WrestleMania, where he was one of multiple wrestlers who came to possess champion Bad News Barrett's title belt while defeating Barrett in non-title matches. Bryan announced his entry into the multi-man ladder match for the Intercontinental title at WrestleMania on the March 12 episode of SmackDown. Bryan won the Intercontinental Championship ladder match at WrestleMania 31. This made him one of only six wrestlers at the time to achieve WWE's new "Grand Slam" due to winning every active title in WWE (except for female-exclusive titles). At the Raw after WrestleMania 31, Bryan defeated Dolph Ziggler for his first successful title defense.

Following the April 14 SmackDown taping, WWE pulled Bryan from wrestling on the remainder of WWE's touring of Europe as a "precautionary measure". Bryan's scheduled title defense at Extreme Rules on April 26 against Bad News Barrett was later cancelled as Bryan was "medically unable to compete". Less than a week later, WWE stopped advertising Bryan from all future live events or television tapings. After about a month off television, Bryan returned on the May 11 episode of Raw. However, he announced that after having gone through MRI, he would be out for an unknown period of time, and might not even wrestle again; the nature of his injuries were not revealed. Therefore, he relinquished the Intercontinental Championship. However, on the Elimination Chamber pre-show, he stated that he would eventually return to the ring. In June, Bryan was announced as a judge for WWE Tough Enough. Bryan returned to WWE TV on the August 10, 2015 episode of Raw, where he was guest on MizTV. During the segment, Big Show and a returning Ryback cleared The Miz out of the ring, and Ryback clotheslined Big Show as Bryan celebrated with Ryback.

After several more months of inactivity, Bryan officially announced his retirement on the February 8, 2016 edition of Raw. In July, Bryan began hosting the WWE Cruiserweight Classic with SmackDown announcer Mauro Renallo. Bryan was appointed as the General Manager of SmackDown LIVE by SmackDown Commissioner Shane McMahon on the July 18, 2016 episode of Raw. Along with McMahon, Bryan played a vital role in the WWE draft with the duo selecting WWE Champion Dean Ambrose as their overall first pick for SmackDown. At Battleground, Bryan appeared during the Social Media Lounge segment with host Tom Phillips, discussing his role as General Manager of SmackDown along with Raw General Manager, Mick Foley. Bryan made multiple appearances throughout the night, including with Dean Ambrose to end the pay-per-view after the champion successfully defending the championship against Seth Rollins and the returning Roman Reigns of the Raw brand in a triple threat match up. Bryan regularly appears on Talking Smack, a post-SmackDown interview show on the WWE Network. On the August 23 episode of Talking Smack, The Miz went on a tirade against Bryan for calling him a coward with Miz calling Bryan the coward for not returning to the ring when he promised the fans he would. Later that month Bryan would book Miz in a match against Dolph Ziggler at WWE Backlash with the Intercontinental Championship on the line. The two would continue to feud on WWE television into the month of September with Miz often running away from Bryan when a physical altercation would be teased. On September 14 the Crusierweight Classic finale aired live on the WWE Network with Bryan on commentary in an event which saw TJ Perkins crowned the first ever WWE Crusierweight Champion.

With the inception of WWE's second brand split, Bryan was appointed by SmackDown General Manager on the July 18 episode of Raw. Along with SmackDown commissioner Shane McMahon, Bryan played a vital role in the WWE draft. After SummerSlam on August 21, Bryan unveiled two new championships exclusive to the SmackDown brand: the SmackDown Women's Championship and the SmackDown Tag Team Championship. As part of his General Manager duties, Bryan co-hosted Talking Smack with Renee Young, a post-show interview segment on the WWE Network. The segment frequently became the site for heated altercations between Bryan and The Miz; Bryan openly expressed his disdain while Miz complained about being mistreated. The two continued to feud for the rest of the year, with Miz often running away from Bryan when a physical altercation was teased. These altercations were intertwined with Miz feuding over the Intercontinental Championship with Dolph Ziggler. Following another verbal clash on Miz TV at the November 1 episode of SmackDown, Bryan decided to trade Miz to Raw if he failed to regain the championship from Ziggler. Miz defeated Ziggler on the 900th episode of SmackDown on November 15 to become a six-time Intercontinental Champion.

On the October 11 episode of SmackDown, Bryan and Shane challenged the Raw brand to three 5-on-5 traditional Survivor Series elimination tag team matches at the event of the same name as a means to determine which brand was superior. On the October 17 episode of Raw, Raw Commissioner Stephanie McMahon and Raw General Manager Mick Foley accepted Bryan's challenge.

On the April 10 and 11, 2017 episodes of Raw and SmackDown, Bryan was involved in the 2017 Superstar Shake-up in which brand's former champions Alexa Bliss, Bray Wyatt, Dean Ambrose, The Miz, Heath Slater and Rhyno were traded to Raw. Bryan later took time off from WWE television for paternity leave and returned on the June 20 episode, during which he stripped Carmella of her Money In The Bank briefcase and suspended James Ellsworth due to his interference in the match. On the August 1 episode of SmackDown, Bryan appointed Shane McMahon as a guest referee for United States Champion AJ Styles's title defense against Kevin Owens at SummerSlam, thereby triggering a long-term feud between Owens and Shane that would ultimately also involve Bryan himself.

Bryan was again absent from television after being attacked by Kane on the October 30 episode of Raw. He returned on the November 14 episode of SmackDown.

After Survivor Series Bryan became deeply involved in Shane McMahon's feud against Kevin Owens and Sami Zayn, favoring the latter two. On the November 21 episode of SmackDown Shane was about to fire the two for attacking him during their Survivor Series interbrand elimination match against Team Raw, which SmackDown ultimately lost. To settle the dispute whether Owens and Zayn should be fired, the two were scheduled to wrestle Randy Orton and Shinsuke Nakamura at Clash of Champions with Owens's and Zayn's jobs on the line. During the match Shane and Bryan acted as guest referees and come to blows: after Shane intentionally stopped a count at two during a pinfall attempt by Zayn, while Bryan made a fast count to give Owens and Zayn the win. Over the following weeks, Bryan kept on favoring Owens and Zayn by giving them multiple opportunities at AJ Styles's WWE Championship, first in a handicap title match at the Royal Rumble and then by including Owens and Zayn among the five challengers at Fastlane. During the latter match, Shane broke up pinfall attempts by Owens and Zayn, resulting in a brutal attack by Owens and Zayn on the following SmackDown.

At that time, after more than two years of evaluations, reviews of his medical history and neurological and physical evaluations, Bryan was cleared by three external independent neurosurgeons, neurologists, and concussion experts (in addition to Joseph Maroon) to return to WWE in-ring competition on March 20. On that day's SmackDown Live, Bryan thanked fans for their constant support and vowed to wrestle again. In his role as General Manager, he (kayfabe) fired Kevin Owens and Sami Zayn for attacking Shane McMahon the week before, resulting in Owens and Zayn attacking Bryan. In response, Bryan expressed regret over favoring them and scheduled a tag team match at WrestleMania 34 pitting himself and Shane against Owens and Zayn, with the latter being rehired if they win. At WrestleMania on April 8, Bryan and McMahon won after Bryan made Zayn submit in his first match since April 2015. As a result of being medically cleared, Bryan resigned as general manager.

Bryan participated in the 50-man Royal Rumble match at the Greatest Royal Rumble event as the first entrant, lasting for 76 minutes—the record for longest time in a Royal Rumble match—before being eliminated by Big Cass in the final three. Bryan defeated Cass at Backlash on May 6 and Money in the Bank on June 17. On the June 26 episode of SmackDown Live, Bryan was aided by Kane in a post-match attack from The Bludgeon Brothers, thus reuniting Team Hell No. At Extreme Rules, Team Hell No lost to The Bludgeon Brothers, after Kane was attacked pre-match with Bryan having to compete in a handicap match.

After months of goading and later avoiding Bryan—as well as getting involved in Team Hell No's feud with The Bludgeon Brothers—Bryan competed against long-time rival The Miz at SummerSlam, but lost due to an undetected use of brass knuckles. Following SummerSlam, Miz mocked Bryan by delivering a fake retirement speech and Bryan's wife Brie Bella returned as his partner. At Hell in a Cell on September 16, Bryan and Bella lost to Miz and Maryse after Maryse pinned Bella. At Super Show-Down on October 6, Bryan defeated Miz to earn a WWE Championship opportunity against AJ Styles at Crown Jewel on November 2. However, in wake of the Khashoggi death incident he refused to work the Crown Jewel event in Saudi Arabia and the storyline was altered so that their match took place on the October 30 episode of SmackDown Live, which Bryan lost. On the November 6 episode of SmackDown Live, Bryan was named team captain of SmackDown at Survivor Series on November 18, but later had to share this role with The Miz.

Bryan as WWE Champion in January 2019

On the November 13 episode of SmackDown Live, Bryan defeated AJ Styles to win the WWE Championship for the fourth time following a low blow. After the match, he attacked Styles, turning heel for the first time since 2012. As a result of his title win, Bryan was removed from Team SmackDown at Survivor Series with Jeff Hardy taking his place on the team. Instead, he faced WWE Universal Champion Brock Lesnar in an interbrand champion vs. champion match, which he lost. Two days later on SmackDown Live, Bryan explained his actions, stating that he was following his dreams and that the fans were not with him during his recovery to return to the ring. He then christened himself as "The New" Daniel Bryan, and a rematch between Bryan and Styles for the title was scheduled for TLC: Tables, Ladders & Chairs, where he successfully defended the title. At the Royal Rumble on January 27, 2019, Bryan successfully retained his title against Styles once again, this time following interference from the returning Rowan. On the January 29 episode of SmackDown Live, Bryan threw the standard title belt in a garbage can (bemoaning the fact it was made from leather) and introduced a new belt, made from "entirely sustainable materials". Bryan was then scheduled to defend his championship in an Elimination Chamber at the Elimination Chamber event on February 17, where he successfully retained the title by last eliminating Kofi Kingston. At Fastlane, Bryan was originally scheduled to defend his championship against Kingston, but after Mr. McMahon replaced Kingston, Bryan successfully retained the title in a triple-threat match against Kevin Owens and Mustafa Ali. Bryan eventually defended the championship against Kingston at WrestleMania 35, where Bryan lost, ending his fifth world championship reign at 145 days. After WrestleMania, Bryan was briefly sidelined by an undisclosed injury, but was cleared to return to action on April 30. On May 6, Bryan competed on his first match on Raw since March 2015, where he lost to Kingston in a WrestleMania rematch, ending their feud.

On the May 7 episode of SmackDown Live, Bryan and Rowan defeated The Usos for the vacant WWE SmackDown Tag Team Championship, marking their first reign as a team. At Money in the Bank, Bryan and Rowan faced off against The Usos in a non title match in a losing effort. At Stomping Grounds, Bryan and Rowan defeated Heavy Machinery (Otis and Tucker) to retain the titles. On July 14 at the Extreme Rules pay-per-view, Bryan and Rowan lost the titles to The New Day (Big E and Xavier Woods) in a triple threat tag-team match, which also involved Heavy Machinery.

In August, Bryan and Rowan became involved in a storyline with Roman Reigns, as Reigns was being targeted for attacks by a mystery conspirator. Reigns suspected Rowan as his attacker due to seemingly incriminating video footage, but Bryan instead revealed that the attacker was merely a man who resembled Rowan. However, Rowan later turned on Bryan and revealed that he was the attacker the entire time, ending the alliance between the two. On the September 24 episode of SmackDown Live, Bryan was saved by Reigns from an assault from Rowan and Luke Harper. Bryan then joined with Reigns to take down Rowan and Harper, thus turning face in the process. At Hell in a Cell, Bryan teamed with Reigns to defeat Rowan and Harper.

On the November 8 episode of SmackDown, Bryan was attacked by Universal Champion "The Fiend" Bray Wyatt. In response, Bryan challenged Wyatt for the Universal Championship at Survivor Series, which Bryan lost. On the following SmackDown, after Wyatt challenged Bryan to another match, Bryan accepted the challenge and said that the Yes Movement is back. During the Yes chants, Wyatt appeared as The Fiend and attacked Bryan, ripping out his hair and beard. Bryan, sporting a clean shave and hair cut short, returned at TLC: Tables, Ladders & Chairs to attack Wyatt. On the December 20 episode of SmackDown, Bryan defeated The Miz and King Corbin in a triple threat match to earn another Universal Championship match at the Royal Rumble on January 26, 2020, but Bryan was again unsuccessful at the event.

After the Royal Rumble, Bryan began a rivalry with Drew Gulak, who claimed to have "found holes in Bryan's game". This led to a match being made for the Elimination Chamber pay-per-view on March 8, which Bryan won. On the March 13 episode of SmackDown, Bryan formed an alliance with Gulak, as Gulak managed Bryan during his match against Cesaro, where both were subsequently attacked by Cesaro, Shinsuke Nakamura, and Intercontinental Champion Sami Zayn. On the March 27 episode of SmackDown, after Gulak defeated Nakamura, Bryan earned an Intercontinental Championship match against Zayn at WrestleMania 36, which he lost. At the Money in the Bank event on May 10, Bryan competed in the Money in the Bank ladder match, but was unsuccessful as the match was won by Otis. On the May 15 episode of SmackDown, Bryan defeated Gulak in the quarter finals of a tournament for the vacant Intercontinental Championship. On the May 29 episode of SmackDown, Bryan then defeated Sheamus in the semi finals who replaced Bryan's scheduled opponent Jeff Hardy, who was arrested for crashing his car into Elias and who had won a battle royal to face Bryan. Bryan ultimately lost to A.J. Styles in the finals on the June 12 episode of SmackDown.

After taking a hiatus, Bryan returned on the October 16 episode of SmackDown. On the TLC: Tables, Ladders & Chairs pre-show on December 20, Bryan teamed with Big E, Chad Gable and Otis to defeat Sami Zayn, King Corbin, Shinsuke Nakamura and Cesaro in an eight-man tag team match. Following this, Bryan then participated in the 2021 Royal Rumble match on January 31, but was eliminated by Seth Rollins. The next month, Bryan competed in an Elimination Chamber match at the Elimination Chamber event, where the winner would receive a match for the Universal Championship immediately. Bryan won the match, but was quickly defeated by Universal Champion Roman Reigns. Bryan would subsequently request a rematch from Reigns, which he would receive at Fastlane on March 21, in a match where Edge was the special guest enforcer. In the main event of Fastlane, Bryan was defeated by Reigns after Edge had attacked both men with a steel chair. Afterwards, it was announced that Bryan would again challenge Reigns for the Universal Championship at the main event of night 2 of WrestleMania 37, in a triple threat match also including Edge. At WrestleMania 37, Bryan failed to win the title after Reigns pinned both him and Edge. On April 30, he lost to Reigns in a championship vs. career match, meaning that he became banished from SmackDown. On May 4, it was reported that his contract with WWE had expired, and that WWE was "pushing hard" for him to sign a new one.