Editing Professor X (section)

===Messiah Complex===
While using [[Cerebra (Marvel Comics feature)|Cerebra]] and talking to Beast during the ''[[X-Men: Messiah Complex|Messiah Complex]]'' storyline, Charles detects a new mutant so powerful it fries Cerebra's system. He asks Cyclops to send out a team to find out about the mutant. Once the team has come back empty handed, he argues with Scott for not telling him about the team he deployed to find former Acolytes. Scott tells him outright that he does not need him to run the X-Men anymore.<ref>''X-Factor v2 26'' (2008)</ref> This upsets Charles and annoys him later on when he overhears Cyclops briefing X-Factor on the situation.{{Volume needed|c=y|date=August 2010}} He also approaches the [[New X-Men (2004 series)|New X-Men]] in an attempt to help them figure out a non-violent way to help against the Purifiers, but is quickly rebuked by [[Surge (Marvel Comics)|Surge]], who questions where he was when they were getting attacked the first time, and that they did not need to learn from him. Charles questions Cyclops' decision to send X-Force to hunt down his own son, Cable, in front of the students. Cyclops then tells Xavier that he is a distraction that will keep getting in the way and that he must leave the mansion. Xavier is contacted by [[Cable (comics)|Cable]], who lost the mutant newborn to the traitorous actions of [[Bishop (comics)|Bishop]], who in turn lost the child to the [[Marauders (comics)|Marauders]], and tells him that he is the only one who can help Cable save the future.<ref>''Uncanny X-Men #494''</ref> In the final fight, Xavier is accidentally shot in the head by Bishop. Immediately afterward Xavier's body disappears and Cyclops declares that there are no more X-Men.<ref>''X-Men'' #207 - Messiah Complex</ref>

Professor Xavier survives Bishop's gunshot but falls into a coma.<ref>''X-Men Legacy'' #208</ref> Xavier is kidnapped by Exodus, Tempo, and [[Karima Shapandar]]. Exodus tries to heal Xavier, Xavier mentally fights Exodus. Exodus finally approaches Magneto, who is apparently still depowered, for help. Magneto and Karima Shapandar are able to stir Xavier's memories and coax him out of his coma, though Xavier remains slightly confused and partly amnesiac. Later, Exodus confronts Magneto about [[Joanna Cargill]]'s injury (Magneto was forced to shoot a laser through her eyeball to prevent her attempted an assassination of Xavier). Exodus nearly kills Magneto, and Xavier drags Exodus onto the Astral Plane, putting Xavier's own newly restored mind at stake. Xavier defeats Exodus after a harrowing psionic battle, and Exodus reveals the reason he abducted Xavier and to restore his mind: Exodus wants Xavier to lead the Acolytes and find the mutant messiah child (now under the guardianship of Cable) to indoctrinate the child into their cause. Xavier refuses. [[Emma Frost]]'s telepathy picks up on the psychic fight, and Emma informs Cyclops that Xavier is alive. Xavier parts company with Magneto and Karima to try to regain his lost memories by visiting people from his past.<ref name="X-Men Legacy #210">''X-Men Legacy'' #210</ref>

The first person Charles visits is Carter Ryking, who had gone insane after losing his powers. Charles reads Carter's memories and discovers that when the two were children they were used as test subjects by [[Mister Sinister|Nathan Milbury]] of the Black Womb Project, with the approval of Charles' father, Doctor Brian Xavier. Xavier makes the connection Milbury and X-Men villain, [[Mister Sinister]], who has apparently long been manipulating Charles' life in addition to other X-Men. Afterwards, he discovers he has been targeted by assassins.<ref name="X-Men Legacy #211">''X-Men Legacy'' #211</ref>

Charles eventually discovers Mister Sinister had set up Charles, Sebastian Shaw, Juggernaut, and Ryking (Hazard) as potential new hosts for Sinister's mind.<ref name="X-Men Legacy #210"/> Bleeding slowly to death, he apparently gives in to Sinister becoming the new Mister Sinister. But in reality, Xavier is still battling Sinister for control of his body.<ref name="X-Men Legacy #210"/> As Sebastian Shaw and Gambit destroy Sinister's Cronus Machine, the device that he used to transfer his consciousness into new hosts, Xavier drives Sinister out of his body permanently.<ref name="X-Men Legacy #211"/> Xavier thanks Shaw and Gambit for their help and declares he must go and see Cyclops immediately.<ref name="X-Men Legacy #214">''X-Men Legacy'' #214</ref> Professor X returns to the X-Mansion to find it destroyed after recent events.<ref name="X-Men Legacy #214"/> Afterwards, Xavier leaves the ruins of the X-Mansion to secretly meet up Cyclops by psychically coercing his former student for the visit. Xavier explains to Cyclops about the recent events with Mr. Sinister and tries to explain to Cyclops how Sinister has been manipulating Scott's and Jean's lives since when they were children. Xavier attempts to have Scott give him permission to scan Scott's mind for traces of Sinister's influences, but instead, Scott turns the tables on Xavier by revealing that he has secretly invited Emma Frost into their entire meeting and also into Xavier's mind.<ref>"X-Men Legacy" #215</ref>

While in his mind, Emma forces Xavier to relive each of his morally ambiguous decisions under altruistic pretenses. As the issue continues, Charles realizes his human arrogance and that while some of his decisions were morally wrong, he must move forward with his life and deal with the consequences. Emma ends her incursion into Xavier's mind by reminding him of Moira MacTaggert's last words. As he reflects on Moira's words, Xavier gives Cyclops his blessing to lead the X-Men and leaves to find his own path.<ref>''X-Men Legacy'' #216</ref> Following his encounter with Wolverine (in the "Original Sin" Arc) Professor Xavier seeks out his step-brother, the unstoppable Juggernaut in an attempt to reform him. After a conversation about the meaning of the word "Juggernaut" and a review of Juggernaut and Xavier's shared history Xavier offers Cain an empty box as a gift. Confused by Xavier's gift Cain attempts to kill the Professor bringing an entire sports bar down over their heads in the process. Later Cain battles the X-Men in his full Juggernaut armor and conquers the planet. Just as everything appears to be under the Juggernaut's control Xavier reappears and informs him that everything that has just taken place except for Juggernaut destroying the bar took place in Cain's mind. A baffled Cain demands to know how Xavier managed to overcome his psychically shielded helmet to which the Professor replies that he decided to visit Cain in his sleep. Professor Xavier then informs him that he now understands Cain as a person and that he will not attempt to get in his way or reform him again. But Xavier also warns Cain that if he gets in the way of the Professor's path to redemption Xavier will stop him permanently.<ref>''X-Men: Legacy'' #219</ref> Following his encounter with Cain it has been revealed that Xavier is now searching for Rogue.<ref name="X-Men Legacy #220">''X-Men Legacy'' #220</ref>

After his bruising encounter with Cyclops and Emma Frost, Professor X is forced to revisit the biggest challenge and the biggest failure of his career, Wolverine, when the feral mutant asks for Charles' help in freeing his son from the clutches of the Hellfire Club. As the two search for Daken, Wolverine reveals that when he first joined the X-Men he attempted to assassinate Xavier due to some unknown programming. In response, the Professor broke Logan's mind and rebuilt it so that any and all programming he received was forgotten. Logan also revealed that the real reason Xavier asked him to join the X-Men was that Charles "needed a weapon".<ref>''X-Men Legacy'' #217</ref> Eventually Professor Xavier and Wolverine locate Sebastian Shaw's mansion and attack his minions, just as they are about to enter a bomb explodes from within catching them both off guard. From the wreckage emerges an angry Sebastian who immobilizes Wolverine. Meanwhile, Miss Sinister knocks [[Daken]] unconscious and has him taken to the med lab in the mansion's basement. As Shaw prepares to deliver a killing blow to Xavier, Wolverine recovers and stops him telling Xavier to rescue his son. Professor Xavier locates the med lab and after a quick psychic battle with Miss Sinister enters Daken's fractured mind. While in Daken's mind Xavier discovers Romulus's psychic tampering and comments that Daken's mind is even more broken than Wolverine's was. Before Xavier can heal Daken a psychic bomb explodes causing Xavier to become comatose and Daken to wake up. Miss Sinister arrives and attempts to manipulate Daken who reveals that the psychic bomb in his head restored his memories and stabs Miss Sinister in the chest. Meanwhile, Wolverine defeats Shaw and enters the mansion to find Daken standing over an unconscious Xavier preparing to kill him.<ref>''X-Men Legacy'' #218</ref> Wolverine tells Daken that he will not let him hurt Xavier and the two fight. Overcome with guilt over what happened to Daken and Itsu, Wolverine allows himself to be beaten. Just as Daken appears to have won Xavier pulls both of them onto the astral plane revealing that the psychic bomb had little effect on him because his psyche was already shattered. Xavier then explains to Wolverine and Daken that Romulus is solely responsible for Itsu's death and that he lied to Daken about everything because he wanted Wolverine to become his weapon. As the three converse, Daken returns to the physical plane and prevents Shaw from killing Xavier. With the truth revealed Wolverine and Daken decide to kill Romulus. As the two depart Wolverine tells Xavier that he forgives him for all of the dark moments in their history. Wolverine acknowledges that Professor Xavier allowed him to become a hero. Wolverine then tells the Professor that he hopes he will one day be able to forgive him for choosing to kill Romulus.<ref>''Wolverine: Origins'' #30</ref>

Professor Xavier recruits [[Gambit (Marvel Comics)|Gambit]] to go with him to [[Australia]] to find and help Rogue who is currently staying at the X-Men's old base in the Outback; unaware Danger is using Rogue as a conduit for her revenge against him.<ref name="X-Men Legacy #220"/>

In a prelude to the "[[Secret Invasion]]" storyline, Professor X was at the meeting of the Illuminati when it came to the discussion about the Skrulls planning an invasion by taking out Earth's heroes and posing as them. He claims he was unable to distinguish that [[Black Bolt]] had been replaced by a [[Skrull]], and his powers were tested quickly by the Black Bolt Skrull. Professor X leaves after learning even he can no longer trust the others, yet appears to have severely restricted the number of people he informs of the forthcoming alien invasion, as the X-Men were not prepared for the Skrulls, at least at first.<ref>''New Avengers: Illuminati'' #5. Marvel Comics.</ref>  Xavier has not seen again during the events of ''Secret Invasion'', though his X-Men in San Francisco are successful at repelling the invaders there through the use of the modified Legacy Virus.