#1 - Self Possessed 8.93
Season 3 - Episode 8
Rogue appears to have problems with her powers, as the residual impressions of everyone she has touched start flashing through her mind and body.
#2 - Blind Alley 8.88
Season 3 - Episode 5
Mystique escapes from imprisonment while the X-Men repair and rebuild the Institute. Disguised as Alex, she lures Scott into a trap - leaving him stranded in the middle of the Mexican desert without his glasses.
#3 - The HeX Factor 8.83
Season 2 - Episode 15
Mystique breaks a mysterious young girl out of an asylum and brings her to the Brotherhood House.
#4 - Ascension (2) 8.82
Season 4 - Episode 9
The four teams fight a losing battle against their horsemen, until Apocalypse moves his plan to the next level. The tops of the pyramids come off and line the Earth's atmosphere, connected to each other by some sort of energy. Pressed for time, the teams become desperate. The Brotherhood joins the team in Mexico to fight Magneto, and Jean amplifies her power with Cerebro to battle Xavier psychically. Apocalypse lies down in his original resting place, and the evolution of humankind begins. But in the last moments of the battle, Rogue shows up with Leech, and she takes his power and negates Apocalypse's power, ending the evolution before any harm is done. Apocalypse is shut into his machine and sent to another time period, and the horsemen fall out of their trances. Rogue and Kurt give Mystique the cold shoulder, and the episode ends with Xavier deeply disturbed after seeing glimpses into the future of the X-Men, and seeing Jean become the Phoenix, among other changes.
#5 - Operation: Rebirth 8.79
Season 2 - Episode 11
Magneto steals the remaints of the top secret "Rebirth" project, a project Wolverine helped shut down all the way back in World War II.
#6 - Mainstream 8.74
Season 3 - Episode 3
During the rebuilding of the manor, Kitty and Kurt intercept a bunch of graffiti artists disguised as monsters. The older students get to go back to Bayville High for one day before attending a hearing to determine their ultimate fate, while they are banned from using their powers.
#7 - The Cauldron (2) 8.70
Season 1 - Episode 13
Magneto reveals the his plans for the winners of his challenge - to fully unlock their powers with a machine he has built. Back at the mansion, those left behind regroup, and decide to pay Magneto a little visit.
#8 - The Toad, The Witch and The Wardrobe 8.69
Season 3 - Episode 7
Wanda receives a clue from one of Magneto's minions, Pyro, directing her to a ski resort. Meanwhile, Kurt is meeting Amanda's parents for the first time, and the Toad believes he can use Kurt's holo-inducer to disguise himself and win Wanda's love.
#9 - Day of Recovery 8.66
Season 3 - Episode 1
The X-Men and Brotherhood deal with the after math of the world finding out about mutants. Mystique, diguised as Professor X, manages to blow up the Insitute. Some of the X-Men and Brotherhood were captured, leaving the mutants that escaped to find them and the Professor.
#10 - Day of Reckoning (1) 8.65
Season 2 - Episode 16
Wolverine suddenly vanishes, as the Brotherhood members team up with the X-men to defeat Magneto.
#11 - Day of Reckoning (2) 8.65
Season 2 - Episode 17
The Brotherhood and X-men arrive where Magneto is with his new allies.
#12 - Shadow Dance 8.64
Season 2 - Episode 13
Forge is working on a device that will enhance Kurt's teleportation powers.
#13 - The Stuff of Heroes 8.63
Season 3 - Episode 2
Rogue and Wolverine duck a squad of soldiers when the nationwide alert goes out against mutants, while Storm and Beast go into a meeting of Congress to defend themselves. Meanwhile Juggernaut goes on a rampage and the X-Men feel obliged to take him down.
#14 - The Cauldron (1) 8.62
Season 1 - Episode 12
As mysterious metal pods appear, picking up the mutants one at a time, Cerebro detects a new mutant in Hawaii: Alex Summers - Scott's believed to be deceased brother.
#15 - Under Lock & Key 8.60
Season 3 - Episode 9
Mesmero mentally controls Gambit into stealing half of the Spider Stone from Angel.
#16 - On Angel's Wings 8.56
Season 2 - Episode 7
Xavier starts worrying about the existence of mutants becoming public knowledge when the media starts reporting multiple sightings of a man with angel wings. With most of the X-men on Christmas leave, and Cerebro down for repairs, Scott and Rogue are left having to track the man down themselves.
#17 - The Stuff of Villains 8.54
Season 3 - Episode 4
Wanda goes searching for Pietro. Meanwhile the brotherhood's members are expelled from school, much to Lance's dismay.
#18 - Dark Horizon (1) 8.52
Season 3 - Episode 12
As Jean's and Scott's graduation day approaches, Rogue suddenly leaves the mansion.
#19 - Fun and Games 8.52
Season 2 - Episode 4
A malfunction in Juggernaut's stasis field leaves the X-Men without adult supervision. Deciding to hold a party, they ditch Scott and Jean in the wilderness. However, things soon get out of control, when one of the guests gives himself access to Cerebro.
#20 - Dark Horizon (2) 8.47
Season 3 - Episode 13
As all the monsters in the tomb attack, the teammates fight to survive and find a way out.
#21 - Grim Reminder 8.45
Season 1 - Episode 11
A news report from the Canadian mountains triggers something deep inside Wolverine, and he starts having berserk fits. To find out why, he takes the Blackbird to the site, not knowing that Kitty and Kurt are sitting in the back.
#22 - Joyride 8.44
Season 2 - Episode 9
Lance comes to the mansion, wanting to join the X-Men. Unfortunately he has a hard time fitting in, and it doesn't get any easier when he gets the blame for some of the other students' nightly joyrides in the various X-Men vehicles.
#23 - Growing Pains 8.43
Season 2 - Episode 1
When Scott and Kurt use their powers to save several people from a car crash, the question of how much they're willing to ignore to keep their powers a secret comes up. Professor X maintains that the world is not ready to know about them, however the other mutants, now without Mystique's guidance, have other ideas...
#24 - SpykeCam 8.42
Season 1 - Episode 8
As an extra credit project, Evan is given a camera to record the ""current events"" in his life. Though most of them aren't keen on being caught on tape, Sabertooth is most definitively interested in the result.
#25 - X23 8.37
Season 3 - Episode 11
A mysterious female assassin terrorizes the X-Mansion, knocking out the X-Men one by one. Wolverine finds out that it is his clone, created by the Dr. Deborah Risman and raised without love by HYDRA, and she wants to kill him because she holds him responsible for her miserable life. Wolverine and X-23, as she is called, square off in a battle that Wolverine does not want to win.