Cena lost the
WWE Championship at the first WWE
pay-per-view of 2006,
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 thrust into a match against
Edge, who cashed in his
Money in the Bank contract — a "guaranteed title match at the WWE Champion of the owners choosing" — and after two quick
spears pinned Cena for the title. Cena's championship reign ended at
280 days, matching the length of previous champion
JBL. Just three weeks later, Cena won the title back at the
Royal Rumble pay-per-view. After winning the Championship back Cena was put in to a
program with
Triple H, during which the crowd again seemed to
boo the intended
face (Cena) and cheer the intended
heel (Triple H). The negative reaction only intensified when he faced
Rob Van Dam (also cashing in a Money in the Bank contract, which he won at
WrestleMania 22) at
One Night Stand in June. Taking place in front of a crowd of mostly "old school"
Extreme Championship Wrestling fans at the
Hammerstein Ballroom, Cena was met with raucous jeering and chants of "Fuck you, Cena", "You can't wrestle", and "Same old shit". When he began peppering different moves into the match the fans responded with a chant of "You still suck". Cena lost the WWE Championship for the second time in 2006 at One Night Stand, being pinned by Van Dam after interference from Edge.
In July, after Edge won the title from Van Dam in a
Triple Threat match that also involved Cena, it re-ignited the feud between he 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 September's
Unforgiven pay-per-view, in a match that had an added stipulation that had Cena lost he would leave the
Raw brand and go to
SmackDown!. He returned his version of the spinner belt on the next night's
Raw. On the heels of the Edge program, Cena was placed in an inter-
brand angle to determine the so-called "Champion of Champions" — or which was the most dominate champion in WWE's three brands.Cena,
King Booker (
SmackDown!'s then
World Heavyweight Champion), and
Big Show (
ECW's then
World Champion) engaged in a mini-feud leading to a
Triple Threat match at
Cyber Sunday in November, 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 (
worked) physical altercation with Federline on
Raw, Federline appeared at Cyber Sunday to hit Cena with the
World Heavyweight Title belt during the main event Triple Threat match, helping King Booker retain his title. 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. In 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 to
FU him. During their feud Cena ended Umaga's "undefeated" streak at
New Year's Revolution before Umaga caused a (
worked) injury to Cena's
spleen, putting a scheduled
Last Man Standing rematch at
Royal Rumble in (
kayfabe) jeopardy. The match did, however, take place and Cena retained his title.
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 team 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) would eventually win the match and the title. 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 title by 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 May's
Judgment Day and then by
pinfall at June's
One Night Stand. Later that summer, prior to
SummerSlam, Randy Orton was named the #1 contender to the WWE championship, starting a feud between the two. Leading up to the pay-per-view Orton delivered a number of sneak-attacks, hitting Cena with three
RKOs, but in the actual match Cena retained the title, winning by pinfall. 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.
On the
October 1 2007 episode of
Raw, Cena suffered a
legitimate torn
pectoral muscle during a match with
Mr. Kennedy while executing a
hip toss. Though he finished the match and the ensuing attack from Randy Orton, surgery the following day found that his pectoralis major muscle was torn completely from the bone, requiring seven months to a year rehabilitation. As a result he was stripped of the title, as announced by Vince McMahon on the next night's episode of
ECW, ending what was the longest WWE Championship reign in over 19 years. His 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.