| No.overall | No. inseason | Title | Directed by | Written by | Original release date |
| 46 | 1 | "The Juggernaut Returns" | Larry Houston | Julianne Klemm | May 6, 1995 (1995-05-06) |
| Juggernaut's life is at risk when someone else uncovers the Ruby of Cyttorak and claims the powers of Juggernaut for himself. |
| 47 | 2 | "A Deal with the Devil" | Larry Houston | Eric Lewald | September 14, 1996 (1996-09-14) |
| Omega Red, the destruction machine from the former Soviet Union and a sworn enemy of Wolverine is thawed and sent two miles beneath the ocean to salvage a disabled, toxic Russian nuclear submarine threatening to break up near Hawaii. His only condition is that Wolverine and Storm go down with him as insurance. |
| 48 | 3 | "Sanctuary" | Larry Houston | Steven Melching & David McDermott | October 21, 1995 (1995-10-21) |
| 49 | 4 | Jeff Saylor | October 28, 1995 (1995-10-28) |
| Part I: Weary of battling for mutant supremacy, Magneto offers to transport all mutants to an orbiting asteroid named Asteroid M where they can live peaceful and human-free lives; however, Fabian Cortez tricks Magneto into an escape pod and launches him into space.Part II: As Magneto plummets helplessly to Earth, Fabian Cortez assumes control of Asteroid M and sends hundreds of missiles toward Earth. Meanwhile, Rogue goes to help the X-Men and tries to find a missing Gambit. Magneto frees himself and returns in time to destroy both the missiles and Asteroid M. Everyone escapes before the asteroid is destroyed and they all return home (Gambit included) Meanwhile, Cortez is rescued from the descending asteroid by Deathbird and Apocalypse. |
| 50 | 5 | "Xavier Remembers" | Larry Houston | Stephanie Mathison | April 27, 1996 (1996-04-27) |
| When Professor X suffers a slight concussion, his powerful psychic mind is suddenly open to manipulation. The Shadow King takes advantage of this and takes possession of Xavier, leaving his mind trapped on the Astral Plane. |
| 51 | 6 | "Courage" | Larry Houston | Michael Edens & Sandy Scesny | September 23, 1995 (1995-09-23) |
| The day Morph rejoins the X-Men, terrorists attack a top-secret, high-tech weapons factory; the alert interrupts his homecoming party. |
| 52 | 7 | "Secrets, Not Long Buried" | Larry Houston | Mark Onspaugh | February 17, 1996 (1996-02-17) |
| When Cyclops flies solo to a tiny, western, desert community to see an old friend, his plane is blasted out of the sky. Injured and unable to use his powers, he struggles into town, only to discover his friend is missing and the town is caught in the grips of a militant, mutant-only, anti-human hate group: the Children of the Shadow. |
| 53 | 8 | "Nightcrawler" | Larry Houston | Len Uhley | May 13, 1995 (1995-05-13) |
| Gambit, Rogue, and Wolverine take a ski trip in Germany. While Gambit & Rogue seem to be largely enjoying each other's company and time together, Wolverine is restless and longs for some action. When he hears reports of a demon hiding in a local monastery, his investigation reveals not a demon, but a mutant, Nightcrawler, whose devilish appearance is in stark contrast to his peaceful and deeply religious nature. Later the townsfolk attack and burn the monastery. The X-Men convince the townsfolk not to fear what they do not understand, Wolverine, too, learns something about the nature of faith. |
| 54 | 9 | "One Man's Worth" | Larry Houston | Richard Mueller | September 9, 1995 (1995-09-09) |
| 55 | 10 | Gary Greenfield | September 16, 1995 (1995-09-16) |
| Part I: Trevor Fitzroy, Bantam, and Nimrod travel back in time to 1959 and kill Xavier as Master Mold ordered them. This creates an alternate present timeline, where a mutant-sentinel war has destroyed everything. Bishop and Shard arrive in 'alternate present', where sentinels battle violently against 'The Leader' Magneto, and his followers who include husband and wife Wolverine and Storm. Bishop & Shard recruit Wolverine & Storm to help stop Fitzroy, but they fail.Part II: Failing to stop the assassination of Xavier, Bishop, Shard, Storm & Wolverine travel forward to the future, a future changed so much that Forge's time travel machine has never been tested and Forge has no idea who these four time travelers are. After they convince Forge, they go back a few minutes before Xavier dies and save him. Everything reverts to normal. |
| 56 | 11 | "Proteus" | Larry Houston | Bruce Reid Schaefer | September 30, 1995 (1995-09-30) |
| 57 | 12 | Luanne Crocker | October 7, 1995 (1995-10-07) |
| Part I: Moira MacTaggert is trying to help her son Kevin (Proteus), but when he escapes from Muir Island she calls on the X-Men for help. Proteus who has never been off the island is wreaking havoc while trying to find his father.Part II: When Proteus discovers that his deadbeat dad is a prominent politician, he storms the Union Hall right in the middle of his dad's campaign speech on 'family values.' Proteus tells his father that he is his son, his father denies it and runs off in horror, crying for help. Angered at his father's reaction, Proteus creates havoc, but Charles later calms him down, and he stops the rampage. Then he goes back to Muir Island with Moira MacTaggert. |
| 58 | 13 | "Family Ties" | Larry Houston | Marley Clark | May 4, 1996 (1996-05-04) |
| Shortly after Magneto breaks into the X-Mansion, High Evolutionary and his New Men capture him, Quicksilver, Beast, Wolverine, and Scarlet Witch, to do experiments on them. He also reveals that Magneto is Quicksilver & Scarlet Witch's father. The other X-Men later defeat High Evolutionary and his New Men and save the captured mutants. During this episode, High Evolutionary transformed Wolverine into a werewolf. |
| 59 | 14 | "Bloodlines" | Larry Houston | Len Uhley | October 26, 1996 (1996-10-26) |
| On Halloween, Nightcrawler gets a mysterious message. He is informed that his birth mother (whom he never knew) is in trouble. He turns to the X-Men for assistance. Jubilee is baffled that Nightcrawler wants to help the mother who abandoned him. Nightcrawler admits there has been pain, but his faith in God has helped him overcome her rejection. The plot thickens when one of the team members recognizes Nightcrawler's mother's voice. |
| 60 | 15 | "Lotus and the Steel" | Larry Houston | Ted Pedersen & Francis Moss | February 3, 1996 (1996-02-03) |
| Wolverine, losing control, quits the X-Men and returns to the rural Japan of his younger days, in an effort to find himself. He works peacefully with a former spiritual teacher, the monk Oku, to build a temple. But the neighboring village is about to be attacked by bandits, led by the merciless Silver Samurai, unless payment is made. Some of the villagers want to resist and ask Wolverine for help. Wolverine is torn. This is just the sort of thing he had wanted to leave behind. Wolverine bests the Samurai in single combat by taking advantage of Samurai's habit of teleporting behind him: Wolverine anticipates the move and disables the teleportation device, humiliating Samurai. |
| 61 | 16 | "Weapon X, Lies, and Video Tape" | Larry Houston | David McDermott & Steven Melching | June 11, 1995 (1995-06-11) |
| A cryptic photograph unleashes a flood of maddening and painful memories in Wolverine that threaten to drive him insane. To keep his mind from being torn apart, Wolverine and Beast travel to the one location that may hold the answers to his hidden past; the ruins of the top-secret Weapon X lab where Wolverine's bones were laced with adamantium. There he encounters other former "test subjects" – Sabretooth, Maverick, and Silver Fox – who are suffering similar mental breakdowns. Later they find out that many of their memories were implanted, and their true memories are destroyed with the lab. |
| 62 | 17 | "Have Yourself a Morlock Little X-Mas" | Larry Houston | Eric Lewald & Larry Parr | December 23, 1995 (1995-12-23) |
| As all of the X-Men prepare for a festive Christmas, foster child Jubilee is thrilled. She, Storm, and grouchy humbug Wolverine go last-minute shopping in Manhattan, only to be caught in a life-or-death crisis involving Leech, a young member of the Morlocks. Leech needs a blood transfusion, so Wolverine's blood is given and then Leech gets better. Additionally, Storm agrees to give back to Callisto her title as the Morlock's official leader. |
| 63 | 18 | "Beyond Good and Evil, Part 1: The End of Time" | Larry Houston | Steve Cuden | November 4, 1995 (1995-11-04) |
| 64 | 19 | "Beyond Good and Evil, Part 2: Promise of Apocalypse" | Jan Strnad | November 11, 1995 (1995-11-11) |
| 65 | 20 | "Beyond Good and Evil, Part 3: The Lazarus Chamber" | Michael Edens | November 18, 1995 (1995-11-18) |
| 66 | 21 | "Beyond Good and Evil, Part 4: End and Beginning" | Dean Stefan | November 25, 1995 (1995-11-25) |
| Part I: In 3999, Cable attacks Apocalypse, but Apocalypse steals his time device and uses it to arrive at the axis of time which causes Bishop to be thrown off course and trapped at the axis of time. Present day, Jean and Scott finally get married again. Just as they are driving off after the ceremony, the Nasty Boys kidnap Jean – leaving Scott behind. Shard (Bishop's sister) travels to the present day in search of Bishop and arrives in time to see Mr. Sinister trying to take Xavier.Part II: Apocalypse kidnaps another psychic mutant. Lilandra warns Xavier of Apocalypse, and Xavier determines that he is capturing psychics. In anticipation, Shard and Wolverine go to protect Psylocke. Still, she is kidnapped by Magneto and taken to Apocalypse in the axis of time control center. In 3999, Cable reveals a plan to go back in time.Part III: Cable uses a time-traveling ship to go back to the past but unbeknownst to him he is thrown off course by Apocalypse. Cable lands in the present. The X-Men decide to help him in destroying Apocalypse's Lazarus Chamber. They go back in time to ancient Cairo however Apocalypse predicted this and uses the opportunity to teleport Xavier to the Axis.Part IV: Cable and the X-Men destroy the Lazarus Chamber. They then use Cable's computer and Cerebro to trace a homing device on the Professor to the control axis where Apocalypse reveals his plan to use the psychics to destroy all time and recreate a universe, where he will rule unchallenged. Feeling that he was deceived by Apocalypse, Magneto attacks him when Cable arrives and joins the attack. Apocalypse begins draining the psychics which causes time and history to start to disappear. Bishop sees this and releases the psychics. Sinister & the Nasty Boys retreat. The heroes defeat the 4 horsemen of Apocalypse. In the end, the psychics move Apocalypse to the Astral Plane. Using Cable's time and spaceship, everyone else is returned to the present time at the Mansion. Cable travels back to his time. |