On the August 15 episode of Raw, Laurinaitis would ask Kevin Nash, who returned at SummerSlam after the WWE Championship match and attacked the winner, CM Punk, who would then lose the title to Alberto Del Rio after he cashed in his Money in the Bank briefcase, for a private meeting in his office. On the September 5 episode of Raw, after Triple H fired Nash, Laurinaitis would enter Nash's limo with him, leaving the arena. At Night of Champions, Laurinaitis would try and help CM Punk win (with Punk not wanting the help), but was stopped by The Miz and R-Truth, who would attack both Triple H and CM Punk, believing the whole thing is one big conspiracy. Nash would also interfere in the match after Laurinaitis sent a text at ringside.
On the September 26 episode of Raw, Laurinaitis would advise David Otunga, a Harvard Law School graduate, to help the disgruntled wrestlers with his legal knowledge who are complaining to him about Triple H's decisions and actions as COO. On that week's edition of SmackDown, Laurinaitis and Otunga would sit down with Christian, Cody Rhodes, Dolph Ziggler, Jack Swagger and Vickie Guerrero to discuss the matter.
On the October 10 edition of Raw, Laurinaitis was announced by Vince McMahon as the new Interim Raw General Manager, as the decision by the Board of Directors. That same night, Laurinaitis would fire Jim Ross and reinstate The Miz and R-Truth. After a few weeks of hinting at a face turn, Laurinaitis would ask Alberto Del Rio to get CM Punk disqualified, solidifying his heel status, so Punk could lose the WWE Championship, but was unsuccessful in doing so. On the December 26 edition of Raw, Laurinaitis would place Punk in a gauntlet match, where if one of his three opponents were to pin him, they would receive a shot at the WWE Championship on the following week's Raw. Punk agreed to the match, only if he beat all three, then he would get to face Laurinaitis himself afterward, to which Laurinaitis would agree too. During the match, Laurinaitis would distract Punk, allowing Dolph Ziggler to win the match. The following week on Raw, Laurinaitis would distract Punk once again, allowing Ziggler to win the match by count-out, thus, Punk still retained the championship. John Laurinaitis is set to be the special guest referee at the Royal Rumble between CM Punk and Dolph Ziggler for the WWE Championship. However, Laurinaitis revealed that he is going into the match with every intention to screw Punk out of the title, possibly attempted to screw Punk out of the previous matches in order to get him this far. In addition, he declared himself to be the soon to be Raw General Manager rather than just the Interim General Manager. However in response to this, the Board of Executives believe that Laurinaitis is abusing his power, especially due to the declaration to favor Ziggler in the match and his position as Interim General Manager will be taken under review by Chief Operating Officer Triple H. At the Royal Rumble, Laurinaitis brought in another official to help and allowed Punk to claim a victory over Ziggler. On January 30 edition of Raw, Laurinaitis was set to have a performance review by Triple H. During the review, Triple H would degrade Laurinaitis fully and before he could announce the decision, he was interrupted by The Undertaker. The WWE Board of Directors decided on February 7, 2012 to retain Laurinaitis as Raw's interim General Manager. It was also determined on February 27, 2012 that the respective General Managers of Raw and Smackdown would be changing places for one night only with Laurinaitis in charge of SmackDown for March 9, 2012 and Theodore Long in charge of Raw for March 5, 2012. On that week's edition of SmackDown, Laurinaitis wrestled his first match in 11 years (as well as his first for WWE), losing to Theodore Long in a Singles match.
Following his match against Long, the two began a feud that led up to WrestleMania, in which both Long and Laurinaitis chose six superstars to represent them, the winning team would decide the new General Manager of both respective brands.
At WrestleMania XXVIII, Team Laurinaitis defeated Teddy Long's team, resulting in Teddy Long losing his position as the General Manager of SmackDown, and John Laurinaitis became the permanent General Manager of both brands. After WrestleMania, Laurinaitis used his power against those who were against him, constantly attempting to bend the rules unfairly to the advantage of those who befriended him. On the April 23 episode of Raw, Laurinaitis appointed WWE Diva Eve Torres as Executive Administrator of Raw and SmackDown. On the April 30 episode of Raw, Laurinaitis came to the ring to announce John Cena's opponent for Over the Limit. Laurinaitis, with the aid of Lord Tensai, attacked Cena, and subsequently announced that he will be returning to the ring to face Cena at Over the Limit. On the May 14, 2012 episode of Raw, Laurinaitis fired Big Show from the WWE after Show mocked Laurinaitis' voice, despite Show giving in to Laurinaitis' demands and begging to keep his job. Later in the episode, Laurinaitis received a letter (which was taken away from him and read aloud by Cena) from the WWE Board of Directors stating the rules for his match against Cena at Over the Limit: the match will be one-on-one, Laurinaitis may not appoint a special referee, all superstars are banned from ringside, the only ways to win are pinfall or submission, any WWE employee who interfered in the match will be immediately fired, and if Laurinaitis lost the match, he would be fired. During the match, Laurinaitis made several attempts to run away from Cena before he was finally brought back to the ring by Big Show who eventually helped Laurinaitis win the match via pinfall after hitting John Cena with the WMD. Laurinatis suffered an array of injuries from the match, including a possible concussion and contusions over his body.
Laurinaitis returned the next night on Raw, using a power chair and crutches for mobility purposes. John Laurinatis told everyone that he rehired Big Show in order to help John Laurinaitis win the match against John Cena. On June 4, it was announced by David Otunga, that Mr. McMahon would return that next week to examine Laurinaitis for further evaluation. On the June 11th episode of Raw Mr. McMahon would give him one more chance. At the end of the Raw Supershow The Big Show would give Vince McMahon the WMD just moments before firing John Lauriniatis. On June 15th episode of Smackdown, he gets smacked by John Cena. On the June 17, 2012 "No Way Out" Pay-Per-View, John Cena defeated the Big Show by escaping the steel cage. Then Mr McMahon would say to Big Johnny "YOU'RE FIRED", afterwards he was given an Attitude Adjustment through the announcer's table by John Cena. On the June 18th episode of RAW, John Laurinaitis appeared and stated that he made the main event for the show before getting fired, a 3 on 1 handicap match between the team of him, Otunga, and Big Show vs Cena. Show would not participate in the match and Otunga would leave the match midway through because Laurinatis refused to tag Otunga in twice, leaving Laurinatis to face Cena alone. He was given the Attitude Adjustment 3 times by John Cena.
On July 30, It was announced on WWE.com that Laurinaitis resigned as the Senior Vice President of Talent Operations and returned to being a road agent. Laurinaitis made a one-night-only return at a live event in Doha in February 2013. Laurinaitis returned on the March 29, 2013 edition of SmackDown, offering The Rock his services as manager for his match at WrestleMania 29 against John Cena. Rock would respond by giving Laurinaitis a Spinebuster then a People's Elbow.
He made another appearance at Survivor Series on November 24, 2013 in a backstage segment with R-Truth, Santino Marella, Los Matadores, El Torito and Fandango. He also made an appearance at the 2013 Slammy Awards, presenting the Rookie of the Year award to The Shield. Laurinaitis made another appearance during SmackDown's 15th Anniversary Special on the October 10, 2014 episode of SmackDown in which he formed a team to face Teddy Long's team to be determined as the greatest GM in SmackDown history. His team lost. On March 28, 2015 he made an appearance at the 2015 WWE Hall of Fame where he inducted The Bushwhackers.