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 gimmick: 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, making it to the final six before being eliminated by Big Show. 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 (kayfabe, 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 kayfabe stabbed in the kidney while at a Boston-area nightclub by Carlito's bodyguard, Jesús. This worked injury was used to keep Cena out of action for a month, while Cena was filming The Marine. Immediately on his return 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 STFU (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 at the WWE Champion 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 Triple H. The negative reaction 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, Cena was met with raucous jeering and chants of "Fuck you, Cena", "You can't wrestle", and "Same old shit". 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 worked physical altercation with Federline on Raw, Federline appeared at Cyber Sunday to hit Cena with the World Heavyweight Chamionship 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.
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 the Royal Rumble in kayfabe jeopardy. The match did, however, take place with Cena retaining 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 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 legitimate 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 in to 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 John "Bradshaw" Layfied (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 edition 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 Bragging Rights, Cena defeated Orton in a 60 minute Iron Man match. A stipulation was placed that if Cena lost, he would have had to leave the Raw brand. He lost at TLC by flying through a table, making "The Celtic Warrior" Sheamus the new WWE Champion. At the 2009 Slammy Awards, he beat Randy Orton, to become the Superstar Of The Year .