Strategy X - Scott, Jean, Xavier, Ororo, and Logan are at the Institute. Mystique and Todd are the Brotherhood. Mystique is also the principal of Bayville High. Kurt arrives at the Institute.

The X-Impulse - Kitty discovers her phasing abilities, meets Lance, and somewhat reluctantly joins the X-Men. Lance is recruited to the Brotherhood.

Rogue Recruit - Rogue, living with foster mom Irene, manifests her powers. Mystique impersonates evil X-Men to trick her into joining the Brotherhood.

Mutant Crush - Fred joins the Brotherhood and attempts to date Jean.

Speed and Spyke - Longtime rivals Evan and Pietro discover each other as mutants. Evan is mistakenly incarcerated and later his record is cleared. Pietro also serves time until Magneto busts him out. Evan joins the X-Men and Pietro becomes the newest Brotherhood member.

Middleverse - Kurt's watch breaks after he teleports. Rogue accidentally banishes him to the Middleverse, where he meets Forge. Feeling guilty, Rogue leads the X-Men back to the Middleverse machine, which they successfully reset, freeing Kurt and Forge.

Turn of the Rogue - Mystique pulls strings to get Rogue on a geology field trip in place of Jean. Rogue discovers Mystique along for the ride also, drains her memories, learns how she was manipulated, and defects to the X-Men.

Spykecam - Evan's film project leads Sabertooth to the mansion. Kitty and Rogue act in a school play.

Survival of the Fittest - Mystique releases Juggernaut from his prison, hoping he will help her steal Cerebro. In his quest to get revenge on Xavier, his half-brother, he destroys the device. The X-Men and Brotherhood work together to disarm the supermutant.

Shadowed Past - Rogue has dreams of Kurt as an infant, which turn out to be memories stolen from Mystique. Kurt confronts Rogue in a mostly-empty school hallway, turns off his watch, and teleports away. Desperate to learn about his past, he then answers a mysterious note. Mystique tells him she is his mother. Pietro blows off Mystique's orders to obey Magneto, interrupting the meeting. Logan searches the castle in Rogue's dreams, and finds a recently-destroyed DNA lab.

Grim Reminder - A chip in Logan's brain becomes active, prompting him to return to Canada. Kurt and Kitty accidentally accompany him, and help defeat Sabertooth and the evil scientist. The chip is removed and Logan feels better.

The Cauldron - Scott's long-lost brother, Alex, discovers his powers and falls in with Magneto. Lots of mutants wind up on Asteroid M. Sabertooth, Mystique, Scott, and Alex are artificially evolved to their highest level, but later return to their former states.

Growing Pains - Edward Kelly becomes principal of Bayville High. Risty, a foreign student, befriends Rogue. Nine new students arrive at the Institute. The Brotherhood openly reveal themselves as mutants, destroying the soccer field, school gym, and new hawk mascot in the process. Xavier erases the episode from the public's memory, though he may have missed Kelly.

Power Surge - Jean's powers become suddenly stronger. Hank McCoy, beloved chemistry teacher and coach of random sports, makes an appearance.

Bada-Bing Bada-Boom - Kurt and Tabitha are punished for messing around on a training mission. Tabitha talks Kurt into taking her to the carnival. There her father coerces her into helping steal the proceeds. The Brotherhood, similarly plagued by financial trouble, also make an attempt at the money. Mr. Smith is arrested, Kurt gets a harsher penalty, and Tabitha leaves to join the Brotherhood, where she breaks into Mystique's locked bedroom.

Fun and Games - Xavier leaves to fix a problem with Juggernaut's holding tank. The younger X-Men open the Institute to a party. With Arcade's unwitting help, Risty steals some information from Cerebro, and is then revealed to the audience as Mystique.

Beast of Bayville - Dr. McCoy loses control of his mutation, transforming fully into Beast. He agrees to take a teaching position at the Institute.

Adrift - Scott goes to visit his brother in Hawaii. Kurt messes with his holowatch in an attempt to improve his appearance. The Summers boys are thrown into a very cliché stranded-on-a-boat type sequence until the X-Jet comes to rescue them. Xavier fixes Kurt's watch, but sets the standard projection to 'female'.

Shadow Dance - Forge invents a device to slow down Kurt's teleporting, allowing a look at his alternate dimension and greater distance capabilities. Amanda invites Kurt to the school dance, and he agrees. At the big event, monsters from the other dimension escape through an unsealed portal and terrorize the students. Amanda reveals what she knows about Kurt, claiming to have seen him in Shadowed Past. Forge arrives with a new version of the Middleverse machine and seals away the monsters.

African Storm - An African shaman, intent on stealing Storm's powers, kidnaps her.

Joyride - Lance temporarily joins the X-Men, wanting to be near Kitty. Using him as a scapegoat, several of the New Recruits borrow various X-vehicles. They get busted, and Kurt's punishment details turns over to them.

On Angel's Wings - While their fellow students go home for the holidays, Scott and Rogue head to New York to search for a mysterious angel. They find Warren Worthington, as does Magneto, but he chooses not to join either team.

Mindbender - Mesmero brainwashes Jean, Kurt, Kitty, and Evan, forcing them to steal three rings, which he uses to open a door. Behind this door and two others is Apocalypse, an ancient and powerful mutant.

Walk on the Wild Side - Amara begins classes at the high school. Jean, Rogue, Kitty, Tabitha, and Amara form a vigilante squad called the Bayville Sirens. They are eventually cornered by the police, but a disguised Mystique helps them escape.

Retreat - Beast takes several of the students back to nature, where crypto-hunters mistake him for Bigfoot.

Operation: Rebirth - Logan reveals his memories of World War II to Xavier, including details about his partner, Captain America, and how they helped rescue a young Eric Lehnsherr. Kurt and Rogue accompany him on a mission to the Sahara desert, where Magneto is attempting to make himself youthful once more. Kurt doesn't have the heart to destroy the machine, and in return Magneto spares their lives.

HeX Factor - Mystique rescues Wanda from an asylum and brings her back to the Brotherhood. At the same time, she kidnaps Xavier and takes his place. After some training with a true witch, Agatha, Wanda single-handedly forces the X-Men to retreat from battle. Tabitha leaves the Brotherhood, blowing up Mystique's room on her way out.

Day of Reckoning - Magneto returns with three new Acolytes: Colossus, Pyro, and Gambit. Pietro sells out the Brotherhood to join his father. Mutants are outed on the national news when Trask forces them to battle a Sentinel. Magneto is killed and several mutants from both teams are taken prisoner. Meanwhile, Mystique initiates Defcon 4 and the mansion's self-destruct mode. Scott leads his team to safety and threatens the apparent Xavier, calling out Mystique.

Day of Recovery - The remaining X-Men and Brotherhood members set out to free their captured comrades. Scott abandons Mystique in the enemy base after she refuses to disclose Xavier's location. Several of the New Recruits hide out with the Morlocks. Todd and Wanda discover that Magneto is still alive.

The Stuff of Heroes - The army pursue the mutants, who hide out in a cave. When pressure mounts, they break through enemy lines and follow reports of a rampaging Juggernaut. They confront and defeat him. In the process, Rogue drains some of his memories and learns where Xavier is hidden. They hurry to the maximum security prison and free him. The government is then more friendly towards the mutants.

Mainstream - The X-Men and Brotherhood return to school, a fact most of the other students are not too pleased with. Kurt's identity is still a secret, because the human population of Bayville has a combined IQ of about two-and-a-half. Jean dumps Duncan.

The Stuff of Villains - Wanda enlists Caliban's help to find Pietro, then hunts him down and gets him arrested. Kelly throws the Brotherhood out of school. Evan has increasing difficulty controlling his powers. Remy arrives at the boarding house, bringing orders from Magneto to rescue Pietro. Rogue and Kitty pursue the Brotherhood. Pietro is rescued and appointed leader of his team.

Blind Alley - Mystique lures Scott away from the Institute, steals his glasses, and abandons him in the middle of nowhere. Jean eventually comes to rescue him.

X-Treme Measures - Power-8, a soft drink discovered to be dangerous to mutants, hits the market. Frustrated with the overworld and his inability to control his powers, Evan joins the Morlocks.

The Toad, the Witch, and the Wardrobe - Kurt reluctantly agrees to meet Amanda's parents. Todd, desperate to please Wanda, steals Kurt's holowatch at an inopportune moment and uses it to improve his own looks. In a mixed-up chase bit, Kurt, Todd, Wanda, and Pyro all go to a ski resort. There, Magneto captures Wanda and has Mastermind replace her unhappy memories with cheerful ones. Kurt and Todd rescue her. Amanda's parents forbid her to see Kurt, but she ignores them.

Self Possessed - Risty returns from a supposed holiday, asks about Rogue's mutation, and takes her to a concert. There, Rogue accidentally absorbs Mystique, loses control, and trashes a lot of stuff before running out. The X-Men give chase, eventually realizing that the rampaging mutants are a shape-shifted Rogue. Mystique confesses that she is Rogue's adoptive mother, but the betrayed girl doesn't want to hear it. Xavier helps Rogue drive the other personalities out of her mind, and she goes home to the Institute infirmary.

Under Lock and Key - Magneto brings together the two halves of the Spider Stone, then destroys them. Unfortunately, they were not a key as he had believed, but a guardian. The second door in Apocalypse's tomb opens.

Cruise Control - Tabitha mysteriously reappears, on a Caribbean cruise with several of the X-Men. All are traveling incognito, but are inevitably revealed. The other passengers shun them. The merry mutants make an impromptu excursion to a volcanic island, where Amara's growing powers trigger an eruption. The gang is outed *again*, this time to cheers and applause. Meanwhile, Kurt and Kitty make fun of Scott and Jean's blossoming relationship.

X23 - The 23rd subject in a line of genetic experiments stakes out the Institute. The otherwise nameless girl is created from Logan's DNA, trained in fighting, and emotionally impaired. She knocks out each X-Man before challenging Logan himself. He forges some kind of connection with her and lets her escape before Shield steps in to deal with matters.

Dark Horizon - Under Mastermind's control, Rogue drains every other mutant on the show. Magneto realizes what's happening and interrupts Scott and Jean's graduation to speak to Xavier. Rogue flees; Logan, Sabertooth, and Gambit are instructed to follow her. Magneto and Xavier formulate a plan to defend the final door guarding Apocalypse. Xavier calls on Mesmero's memories (from their battle in "Mindbender") to determine the location of the shrine. A great X-Men/Brotherhood/Acolyte conglomerate heads to the Sphinx in Egypt. They enter, and the statues attack them. While the students battle for their lives, Beast reads hieroglyphs telling the story of Apocalypse, also known as En Sabah Nur. Then the adults find part of the Eye of Ages, and learn that the real tomb of Apocalypse is in Tibet. Conveniently, Rogue and her pursuers are already there. Mystique opens the final door, in the process being turned to stone. Apocalypse then uses Rogue's powers against her, absorbing the essences of the other mutants and growing stronger. The Sphinx-group transport to the real shrine. Apocalypse knocks them all out with a power blast, steals the transporter, and disappears.

Impact - Apocalypse arrives at a Mayan pyramid in Mexico and casts an energy dome around it. This promptly winds up on the news, sending several of the X-Men on a mission to investigate the mysterious, impenetrable field. Their attempts are unsuccessful. Magneto arrives and throws a lot of metal junk at the dome. This irks Apocalypse enough to draw him out, at which point he destroys Magneto. Xavier, unable to help statue-Mystique, gives her to the Brotherhood. Kurt steals her back, determined to find a way to rescue her. He convinces Wanda to set up a meeting with Agatha, who says that only Rogue can help Mystique. She refuses, instead pushing her mother over the cliff, where she shatters.

No Good Deed - In the process of saving themselves from a subway accident that was really Wanda's fault in the first place, the Brotherhood become known as heroes. They hatch a plot to manufacture disasters, thereby ensuring that they can save the day again and stay in the limelight. In the end it backfires - an unexpected second train sets the stage for terrible destruction. The team bails, leaving the X-Men to handle the situation. They don't quite manage it, but Lance returns just in time, dumping the trains underground to contain the explosion. And in other news, Edward Kelly announces his plans to run for mayor.

Target X - X23 is being chased by Hydra, and kills some of their agents.

Sins of the Son - Xavier is reunited with his ex-wife and their son. He is tricked into merging his son's three personalities, leaving the evil one, Lucas, in charge.

Uprising - Evan, with new and improved powers, crusades for mutant rights. Dorian manifests, but his mother won't let him join any team.

Cajun Spice - Remy takes Rogue on a mission to rescue his father.

Ghost of a Chance - Kitty rescues Danielle Moonstar, who joins the X-Men.

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