Graduation Day is the final episode of X-Men: The Animated Series.
In Washington D.C., Henry Peter Gyrich presents a televised diatribe against the dangers mutants posses to ordinary humans to Congress. Gyrich shouts that humans are at war with mutants and unless the Mutant Containment Bill is passed the mutants with destroy them and even gives examples of mutants causing havoc around the world. However, Charles Xavier comes forward (who seems to be ill from battling this legislation for several weeks) and says that if his bill is passed American citizens will be taken prisoner for no other reason then being different. Xavier goes on to say that the terrorist he speaks of were actually mutants that were protecting ordinary humans. However, Gyrich shouts that mutants want to control all normal humans. Gyrich wanders why Xavier cares so much for mutants and voices his suspicion that he is a mutant himself. Gyrich then attacks Xavier with a small energy disruptor which causes Xavier to lose control of his powers and sends out a telepathic blast which exposses him as a mutant. Xavier then passes out and Gyrich is taken away by security. Cyclops, Beast, and Wolverine are in the audience and rush to Xavier's side. Cyclops says that they must get Xavier to the Blackbird immediately. However, As Wolverine picks Xavier up he tells Cyclops that Xavier has died.
As Beast, Cyclops, and Wolverine get Xavier onto the Blackbird, Gambit flies off. As Beast examines Xavier he tells Wolverine this time his sense of smell was wrong and the Xavier still lives. Cyclops then contacts Jubilee and orders her to prepare the infirmary and to get a live video feed to Moira MacTaggert on Muir Island.
On Genosha the mutants Sunfire, Feral, and several other mutants watch a news report on Xavier's attack. Sunfire says that Magneto was right about the humans. Feral replies that it was just one man that attacked Xavier. However, Sunfire replies that even though Xavier was rich, respected, and normal looking he was still attacked. Sunfire then suggests that they go to war with the humans. From afar Magneto listens to the mutants cries for war.
The next day at the Xavier Mansion, Storm assures Jubilee that Professor X can not be in better care then Best and Moira. However, Jubilee believes that since she is so young Storm and the X-Men are just trying to comfort her and she tells them not to treat her like a child. In the infirmay Beast, Cyclops, and Jean Grey are in contact with Moira. Moira delivers heartbreaking news when she reveals that Charles is beyond the help of medical science. However, Beast knows that the Shi'ar have the technology to save Xavier. Moira asks how they can even get in touch with Lilandra since she lives on a distant alien world. Beast suggests that Jean use her telepathic powers to contact Lilandra. However, Jean says that can not telepathically link with Lilandra's mind across the galaxy. She then says that the only reason Professor X is able to communicate with Lilandra is because they have a strong personal bond.
Later that day a news anchor named Trish Tilby reports that all over the world mutants have begun to riot. Trish then reports that these attacks are unorganized and that the mutant rebellion will soon end unless the mutants find a leader. Morph then shapshifts into Xavier and goes on television and says violence is never the answer. However, this is really just Morph disguised as Xavier. Cyclops then says that next they must take care of Magneto.
At that very moment Magneto addresses his followers he gives a speech on how they have all seen the hatred that normal humans have toward them. Magneto then says that the world now belong to mutant kind and that they must take it by force. As the crowd cheers Magneto begins to see his dreams of a war between mutants and humans start.
Back at the mansion the X-Men work on a way to get a message to Lilandra. However, Storm tells Cyclops that the message will take nine months to reach her and that Xavier might not have but only a few hours to live. Cyclops then calls Wolverine into the War Room and tells him that Magneto is building an army that is gathering on Genosha. Cyclops says that he learned of this when Jean used Cerebro. Cyclops tells Wolverine that if they defeate Magneto his followers will lose hope and they can stop the war before it begins. As Jean walks in she offers to use her telekenitic force field to protect them. However, Wolverine knows that this is a suicide mission and attempts to stop her from going with them. However, Cyclops says that arguing with her won't do any good.
Outside the mansion Rogue tells Gambit that she can't believe they are on the brink of war. As they look into the sky the see the Blackbird fly off. As the Blackbird approaches Genosha, Magneto uses his magnetic powers to destroy the jet. However, Cyclops, Jean, and Wolverine jump out before the jet is totally destroyed. Jean then places a telepathic shield around them and they land safely on the ground. As all of the mutants sleep Wolverine, Cyclops, and Jean are bale to sneak into the camp grounds for the mutant army. However, they are soon spotted by Sunfire and Feral. As the other mutants wake up Magneto stands on the balcony of his fortress and says that it is time to attack the humans. While Magneto gives his speech Cyclops, Jean, and Wolverine go to the side of Magneto's mountain fortress and Cyclops uses his optic blast to blast a hole into the side making an entrance to the fortress.
As Magneto continues his speech the X-Men are able to sneak up behind him. As the X-Men attack Magneto, Magneto fights back. As they continue to fight Magneto asks why they continue to fight him after what the humans did to Xavier. As Wolverine lunges at Magneto he says that it is what Xavier would want. Magneto then fires a magnetic pulse at Jean. Jean's powers are then somehow enhanced and her mental blast pushes her back and she hits the wall behind her. Magneto says that mutants must strike first. Cyclops replies that Xavier would never strike first and that he didn't give his life so that Magneto could destroy everything he was trying to accomplish. As Magneto asks what Cyclops is talking about Cyclops answers that Professor X is dying and that he only has a few hours left to live. Magneto then feels sorrow for his friend and tells that X-Men that out of respect for him he will allow them to live. Just then Jean realizes that Magneto's magnetic powers enhanced her own telepathic powers and tells Magneto of this. Jean continues to say that a telepathic message to Lilandra is Xavier's only hope and that Magneto might be able to enhance Xavier's powers aswell. Magneto says that he can not help them because he has an army to lead and that he has dreamed of this moment all his life. However, Cyclops reminds Magneto of how unselfish and kind Xavier is and tells Magneto that Xavier would help him if their situations were reversed.A few hours later at the Xavier Mansion the X-Men cry as they surround Xavier's bed. As Wolverine walks in Jubilee runs to him and gives him a hug. As Cyclops walks in he asks Beast how Xavier is doing. Beast answers that Xavier could pass at any monent and in turn asks if Magneto is ready. As Magneto walks in he asks Beast what he must do. Beast answers that Xavier must make contact with Lilandra but his mind is too weak. Beast instructs Magneto to focus his megnetic energy on his brainwaves. Magneto then places his hands on Xavier's head and exposes his brain to magnetic energy. A beam of light shoots from Xavier's head and goes into space. Afterward Xavier (who is extremely weak) awakens and says hello to his friend, Magneto. As Xavier looks around he personally says goodbye to Magneto and each member of the X-Men. Finally, Xavier says that he is proud of all his X-Men and passes away right before their eyes. Just then a bright light fills the room and Lilndra appears before them. As Lilandra walks up t0 Xavier Magneto tells her that she is too late to save him. However, Lilandra says that by human standards she is late but her people have the technology to bring Xavier back to the land of the living and cure him. Lilandra continues that Xavier will susrive but only under the care of the Shi'ar meaning that he will have to go with her. . . forever. As Lilandra's ship takes off with Xavier, Xavier telepathically communicates with the X-Men and Magneto saying that he will always be with them in spirit. Magneto and the X-Men watch as Lilandra's ship flies into the starry night sky.
|Cedric Smith||Professor X / Charles Xavier|
|Norm Spencer||Cyclops / Scott Summers|
|Cathal J. Dodd||Wolverine / Logan|
|Alison Sealy-Smith||Storm / Ororo Munroe|
|George Buza||Beast / Hank McCoy|
|Tony Daniels||Gambit / Remmy LeBeau|
|Alyson Court||Jubilee / Jubilation Lee|
|Catherine Disher||Jean Grey|
|David Hemblen||Magneto / Eric Magnus Lehnsheer|
|Barry Flatman||Henry Peter Gyrich|
|Lally Cadaeu||Moira MacTaggart|
|Denis Akiyama||Sunfire / Shiro Yoshida|
- Arthur Maddicks
- As Trish Tilby reports on events, the symbol on the news van behind her is that of J3 Communications, the broadcasting company owned by J. Jonah Jameson from Spider-Man: The Animated Series.
- Originally a whole pantheon of Marvel superheroes (possibly including Spider-Man) were to make cameos in this episode, to bid farewell to Professor X. However, this was cut down to just the X-Men bidding farewells.