After his injury healed, Orton joined the Evolution stable, which consisted of Ric Flair, Triple H, and relative newcomer, Dave Batista. The group was pushed on Raw from 2003 to 2004, with the height of their dominance occurring after Armageddon in 2003 when all of the men's titles on Raw were held by the members of Evolution. In 2003, Orton spent much of his time helping Triple H overcome challenges from Kevin Nash, Kane, and former World Championship Wrestling (WCW) superstar Bill Goldberg who were vying with Triple H for the World Heavyweight Championship. Orton joined Triple H in a six-man Elimination Chamber match for the World Heavyweight Championship at SummerSlam but was involved primarily to secure Triple H's title defense and was eliminated by Goldberg.
Afterwards, Orton proclaimed himself "The Legend Killer", a young upstart who was so talented that he touted himself as the future of professional wrestling. He embarked on numerous storyline feuds with "legendary" wrestlers and gained infamy for his blatant disrespect of many older, well-regarded names in wrestling history. He defeated Shawn Michaels at Unforgiven, in the first of many high profile matches billed as "Legend versus Legend Killer", with the help of his stablemate and mentor Ric Flair. Orton then spat in the face of Harley Race on the April 26, 2004 episode of Raw.
During this time, Orton began using the move that would become his signature finisher, the RKO, a jumping cutter, named after his initials. Orton soon defeated Rob Van Dam for the WWE Intercontinental Championship at Armageddon on December 14, 2003. With this win, Orton started the longest Intercontinental title reign in seven years, holding the title for seven months.
Orton continued to establish himself as a "Legend Killer" throughout 2004, challenging the semi-retired wrestler Mick Foley. Famed for his hardcore matches and an ability to handle excruciating pain, Foley offered Orton a hardcore "Legend versus Legend Killer" match if Orton would put his Intercontinental Championship on the line. In a bloody match involving thumbtacks and barbed wire, Orton defeated Foley.
In July, at Vengeance, Edge defeated Orton to win the Intercontinental Championship, ending Orton's seven month title reign. After the loss of his Intercontinental Championship, Orton entered the World Heavyweight Championship scene. After becoming the number one contender on July 26, he cleanly defeated Chris Benoit for the championship at SummerSlam with the added distinction of being the youngest World Heavyweight Champion in WWE history at age twenty-four. Benoit congratulated Orton after the match, shaking his hand for showing the ability to "be a man".
The following night, Evolution threw Orton a mock celebration, only to reveal that they were not pleased with his new victory. While Batista had Orton propped on his shoulders in elation, Triple H gave him a pleased thumbs up and then abruptly changed it to a thumbs-down, which was followed by Batista dropping Orton to the mat. Ric Flair and Batista attacked Orton in the ring as Triple H revealed his jealousy for Orton's title. He ordered Orton to hand over the championship, but he refused, spitting in Triple H's face and hitting him with the title belt. Orton's break-up with Evolution began a new storyline for him as a crowd favorite when he continued to feud with his former stablemates. A month later, Orton lost his championship at Unforgiven. Seeking revenge, Orton lashed out at Evolution members, catching them by surprise during a show by giving them a large cake as a make-up gift, which he came out of it to beat and humiliate the group. After this, Orton experienced another push, becoming General Manager of the Raw brand for a week following a match stipulation at Survivor Series. He continued to feud with Triple H, using his authority to place his opponents at severe disadvantages during title defenses. Orton was granted another chance at the championship in January 2005 but lost a six-man championship Elimination Chamber match to Triple H at New Year's Revolution. On the January 10 episode of Raw, Orton defeated Batista to earn a match against Triple H at the Royal Rumble for the World Heavyweight title. At the Royal Rumble, Triple H defeated Orton to retain the World title.
Orton began an on-screen relationship with Stacy Keibler and briefly feuded with Christian in February 2005. On the February 28 episode of Raw, "Superstar" Billy Graham made an appearance, in which he advised Orton to "go where no wrestler [had] gone before". Orton then produced a copy of SmackDown! magazine, which featured The Undertaker on the cover. Heeding Graham's advice, Orton claimed that he would set himself apart from all other wrestlers by ending The Undertaker's undefeated streak at WrestleMania. Throughout March 2005, Orton taunted The Undertaker, claiming he was unafraid of him. On the March 21 episode of Raw, Orton turned heel once more after he delivered an RKO to his unsuspecting on-screen girlfriend, Stacy Keibler, knocking her unconscious. During Orton's promos, he would immediately run for cover when signs of The Undertaker's appearance were near (lightning, darkness, or smoke). When legend wrestler Jake Roberts advised Orton not to underestimate The Undertaker, Orton performed an RKO on Roberts as well. In the weeks leading up to WrestleMania, Orton became more defiant and unafraid of the Undertaker, taunting and assaulting him in the ring following distractions from his father, "Cowboy" Bob Orton. At WrestleMania 21, however, the heavily hyped match was unsuccessful for Orton, as he lost despite his father's interference.
The following night on Raw, Orton faced Batista, who had become World Heavyweight Champion. Orton stated on-screen that his match with The Undertaker had aggravated a shoulder injury. While sidelined, Orton appeared on Raw and claimed that he was ineligible for the WWE Draft Lottery due to his injury. He was informed by WWE Chairman Vince McMahon that he was indeed a candidate for the draft, leaving a possibility of a return to SmackDown!. Orton returned to WWE programming for the SmackDown! brand on June 16, announcing that he was the second pick in the 2005 draft lottery. He rekindled his feud with The Undertaker, defeating him at SummerSlam following a distraction from his father. Two months later, Orton and his father Bob Orton defeated The Undertaker in a Handicap Casket match. The following month, Orton was a participant in the annual elimination match of Team SmackDown against Team Raw at Survivor Series. In the match, Orton was the last remaining wrestler in the match, as he pinned Shawn Michaels to get the victory for Team SmackDown. At the event, The Undertaker, who had been absent since Orton had apparently killed him on an episode of SmackDown!, returned by emerging from a flaming casket. The feud was finally settled with a Hell in a Cell match at Armageddon, where The Undertaker offered to retire if he lost. On December 16, The Undertaker entered the ring to deliver a promo while one of his druids appeared to be standing in the ring. The Undertaker sustained an RKO from Orton in a surprise attack. The druid revealed himself to be Orton's father, who gave Orton the Undertaker's urn, which, according to the storyline, allowed whomever held it to control The Undertaker. The Undertaker, however, beat both Ortons in a Hell in a Cell match, which ended their nine-month-long feud with The Undertaker.Following Armageddon, Orton entered the January 2006 Royal Rumble as the thirtieth wrestler to enter the match, but he was eliminated by Rey Mysterio. Mysterio won the match and a title shot, and Orton urged him to put the title shot at stake in a match at No Way Out. In the weeks preceding No Way Out, Orton made disparaging remarks about Eddie Guerrero, Mysterio's friend, in an attempt to gain villain heat. Guerrero's death had occurred only months previously, and many fans felt the comments were unwarranted and highly distasteful. Orton won at No Way Out, earning Mysterio's title shot for the World Heavyweight Championship at WrestleMania 22. General Manager Theodore Long re-added Mysterio to the WrestleMania 22 title match, however, making it a Triple Threat match between Orton, Mysterio, and then-champion, Kurt Angle. On April 2, at WrestleMania 22, Orton was pinned by Mysterio, making Mysterio the World Heavyweight Champion and ending their on-screen rivalry.
On April 4, 2006, Orton was suspended for sixty days for "unprofessional conduct." In an interview, Orton stated, "my conduct was unbecoming of a champion, which is what I will be again when I return". To cover for the suspension, a faked injury was devised, where Kurt Angle broke Orton's ankle during a grudge match. In July, Orton said his suspension resulted from smoking marijuana backstage. Orton returned from his suspension in June to the Raw brand, where he engaged in a storyline feud with Hulk Hogan. Orton began cutting promos insulting the aging Hogan and flirted with Hogan's eighteen-year-old daughter Brooke. At SummerSlam, the two met in a "Legend vs. Legend Killer" match, which Hogan won.
After the newly reformed D-Generation X (DX) (Triple H and Shawn Michaels) cost Edge the WWE Championship numerous times, Edge approached Orton and asked him to join forces to defeat the team. Orton, whose championship reign had been ended by Triple H in 2004, agreed, forming the tag team Rated-RKO. The two became the first to defeat DX since their reunion and quickly dominated the Raw brand's tag team division to become tag team champions. As part of the angle, Rated-RKO attacked Ric Flair with steel chairs to enrage DX on November 27. At New Year's Revolution, Rated-RKO faced DX in a title defense, but the match was declared a no-contest when Triple H suffered a legitimate injury during the match.
With Triple H out of action, Rated-RKO continued their on-screen rivalry with remaining DX member Shawn Michaels. Michaels teamed with John Cena to defeat Rated-RKO for the tag team championship on January 29. Orton and Edge suffered a series of losses to Cena and Michaels in the following months, building hatred towards one another. Edge and Orton also became rivals in their goals of achieving the WWE Championship. Neither Edge nor Orton won the Championship, and they lost their claims as number one contenders after a failed match with Cena at Backlash. Orton then continued his "Legend Killer" persona, attacking Shawn Michaels. Using frequent attacks to the head, including an elevated DDT and a running punt to the face, Orton defeated Michaels at Judgment Day. When the kayfabe wounded and concussed Michaels collapsed in the ring, the referee was forced to stop the match and award Orton the victory. Orton continued his attacks when he engaged himself in feuds with Rob Van Dam, Ric Flair, Dusty Rhodes, and Sgt. Slaughter.
On the July 23 episode of Raw, Orton was named as the number one contender at SummerSlam for John Cena's WWE Championship. Weeks before their scheduled bout at SummerSlam, Orton attacked Cena on three separate occasions by performing RKOs on him. At SummerSlam, Orton lost the title match to Cena, who pinned Orton after executing an FU. The following night on Raw, Orton demanded a rematch for the title, but his request was declined by Raw General Manager William Regal. Orton then took his demands to Mr. McMahon, who also refused to give Orton a rematch unless he proved himself. That night, Orton interfered in Cena's match by assaulting Cena and kicking Cena's father, who was at ringside, in the head. Orton was granted his title rematch against Cena at Unforgiven and won by disqualification when Cena refused to stop punching Orton in the corner. Cena retained the WWE title because a title cannot change hands by disqualification. After the match, Cena's father, who was again at ringside, kicked Orton in the head. At No Mercy, Orton was awarded the WWE Championship by Mr. McMahon after Cena was stripped of the title due to an injury the previous week, which also ended the Orton-Cena storyline prematurely. Orton then lost the title to Triple H in the opening match of the show, making Orton's reign the third shortest in WWE history. Later in the night, Orton defeated Triple H in a Last Man Standing match to regain the title, thus becoming a two-time WWE Champion in one night.
Following No Mercy, Orton continued his feud with Shawn Michaels, who made his return on the October 8 episode of Raw and performed Sweet Chin Music on Orton. The two met in a title match at Cyber Sunday after a match was made in which the fans would get to vote on either Michaels, Jeff Hardy or Mr. Kennedy as the opponent. As a result, Michaels was voted to face Orton. In the match, Orton was disqualified when he performed a low blow on Michaels, but Orton retained the title. In a scheduled rematch, Orton successfully defended the title at Survivor Series against Michaels when he performed the RKO on Michaels for the win. The stipulation of the match was that if Michaels used Sweet Chin Music, the match would be stopped and Michaels would never get a chance at the WWE title, but if Orton got himself disqualified, he would lose the title.After weeks of intensity between the two, Orton defeated Jeff Hardy to retain the WWE Championship at the Royal Rumble. Following this, he re-engaged in his feud with John Cena, who had returned from injury and won the 2008 Royal Rumble match. Instead of cashing in his title opportunity at WrestleMania XXIV, Cena decided to face Orton for the title at No Way Out. Orton lost the match after getting himself intentionally disqualified, thus retaining the title. At WrestleMania, Orton retained the WWE Championship in a Triple Threat match involving Cena and Triple H. Orton won the match by pinning Cena after a Pedigree from Triple H. The following month, at Backlash, Orton lost the title to Triple H in a Fatal Four-Way Elimination match, which also included Cena and John "Bradshaw" Layfield. After failing to win the title back at Judgment Day, Orton faced Triple H in a Last Man Standing match at One Night Stand for the title. Orton lost the match and legitimately broke his collarbone.
Just before he made his return, Orton re-injured himself in a motorcycle accident and to keep on-screen exposure he made an unexpected return to Raw at the beginning of September, criticizing all of the champions on the brand. Heel tag team Cody Rhodes and Ted DiBiase took exception to this and tried to gain his respect, to no avail until at the pay-per-view event Unforgiven, the three of them, alongside new recruit Manu assaulted World Heavyweight Champion CM Punk, costing him his title. He made his in-ring return on the November 3 episode of Raw losing to Punk by disqualification, after Ted DiBiase interfered. In retaliation, Orton punted DiBiase in the head. On the December 1 episode of Raw, Orton proposed that he along with Cody Rhodes and Manu form an alliance. The following week, they made it official, by defeating Batista and Triple H, Orton's former stablemates, in a three-on-two handicap match, dubbing themselves The Legacy. On January 25, 2009, Orton won the 2009 Royal Rumble match, by last eliminating Triple H. On the March 2 episode of Raw, Orton challenged Triple H for the WWE title at WrestleMania XXV. At the event, Orton lost the match. Orton, however, won the title at Backlash, in a six-man tag team match, with Cody Rhodes and Ted DiBiase, facing off against Triple H, Batista, and Shane McMahon. At Extreme Rules, he dropped the title to Batista in a Steel Cage match. The following night on Raw, Orton and Legacy attacked Batista, legitimately injuring him in the process and forcing him to vacate the title. On the June 15 episode of Raw, Orton regained the title in a Fatal Four-Way match involving Triple H, John Cena and The Big Show. Orton later lost the title to John Cena in an "I Quit" match at Breaking Point, but defeated Cena to win back the championship in a Hell in a Cell match at the Hell in a Cell pay-per-view in October. At Bragging Rights, Orton lost the title to Cena in a 60 minute Iron Man match. At the Slammys, he beat The Undertaker by cheating, but lost to John Cena, failing to be the Superstar of The Year