Professor Charles Xavier is the founder of the X-Men. While he has minor appearances in the Marvel vs. Capcom series, he is an important character due to his connection with Onslaught and as the leader of the X-Men.
Professor X can be seen in the background of the Danger Room stage, supervising the "training" from a window. In Colossus's ending, Xavier assists in his training and is proud of his student. He is also seen passing in the credits screen behind the playable characters and bosses.
While not seen, Xavier is mentioned by his brother Juggernaut in his ending.
In Chun-Li's ending, Professor X invites her to join the X-Men.
The final boss, Onslaught, is the embodiment of the darkest emotions of Professor X and Magneto. Xavier's conscience called out for heroes to stop Onslaught, summoning heroes from a different world. With Onslaught's demise, the heroes are able to return to their home. Xavier can be seen unconscious in the background after Onslaught's defeat.
Professor X also appeared in Hulk's and Wolverine's endings. In Hulk's ending Captain America sacrifices himself to finish Onslaught and Professor X laments his death. In Wolverine's ending Xavier is distraught for his actions as Onslaught and is comforted by Wolverine.
Like X-Men: Children of the Atom, Professor Xavier can be seen in the Danger Room stage. He also appears as a card in the Heroes & Heralds mode.