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Amphibians and Brimstone...
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Here it is, the Episode Guide.
For some reason I lost my other Ep. Guide page, either by accident, or i've just forgotten where I put it.
Either way, here's a new one with slightly more information. Once again props to  Extreme Evolution for the super nifty info.

Season 1

Episode 1: Srategy X
Nightcrawler arrives at the Xavier Institute as Toad attempts an infiltration.

Episode 2: The X Impulse
Xavier and Jean try to recruit Kitty Pryde into the X-Men, but Avalanche has other plans for her.

Episode 3: Rogue Recruit
Believing herself a danger to others, a mutant known only as Rogue goes on the run, as both the X-Men and Mystique race to recruit her first.

Episode 4: Mutant Crush
Recruited by Mystique, Blob develops a crush and is determined to make Jean his girlfriend at any cost.

Episode 5: Speed and Spyke
Evan and Pietro, fellow students and constant competitors, discover that they are both mutants with super-powers - which increases their competition to dangerous levels.

Episode 6: Middleverse
After accidentally activating one of Forge's old inventions, Nightcrawler gets stuck between dimensions.

Episode 7: Turn of the Rogue
Scott and Rogue must survive a Geology Club field trip into stormy mountains, while realizing that the people they trust most have been lying to them.

Episode 8: Spykecam
Spyke gets an assignment to document teen life events with a digicam - just as Sabretooth attacks the Institute.

Episode 9: Survival of the Fittest
It's survival training, mutant style. But while the X-Men are proving their mettle in the wilderness, the unstoppable Juggernaut escapes from prison to exact a little revenge against his brother - Professor Xavier.

Episode 10: Shadowed Past
Rogue's recurring nightmares lead Nightcrawler to investigate the truth about his past.

Episode 11: Grim Reminder
A dormant computer chip in Wolverine's brain is reactivated, luring him to Canada and to a hidden lab from his past.

Episode 12: The Cauldron 1
As fights break out between good mutants and bad, Scott learns that his brother is still alive after 10 years, and must get to him before Magneto includes him in his dangerous plans.

Episode 13: The Cauldron 2
Magneto's ambitious plan for Mutantkind takes shape upon his fortress, Asteroid M.

Season 2

Episode 14: Growing Pains
Changes are occuring in Bayville. The Institute receives new recruits, who would just about destroy the place; Rogue finds a new friend, Risty Wilde; Bayville High School gets a new leader, Principal Kelly; and the Brotherhood is left looking after themselves. Avalanche and the others decide it's time the whole world know what mutants are really about.

Episode 15: Bada Bing, Bada Boom
Kitty, Wolfsbane, Iceman, Magma, Jubilee, Multiple, Berzerker, Cannonball, Sunspot
Sypnosis: It's time to train the new recruits. However, when Boom-Boom decides she doesn't like rules and does things her way, Kurt ends up getting involved. As the time for the carnival comes, Boom-Boom is confronted by her father, who wants her to steal the profits from the carnival.

Episode 16: Power Surge
Jean's powers are growing. Now, she has to deal with telepathy as well as telekinesis. And some people have thoughts that she just doesn't wanna hear.

Episode 17: Fun & Games
The Professor has an emergency with his half-brother and has to leave the Institute. With Logan and Storm gone, it's up to Scott and Jean to be in charge. But the younger mutants have other plans in mind, which go awry when a computer wiz, Arcade, gets into Cerebro's main systems.

Episode 18: Beast Of Bayville
New chemistry teacher and gym coach, Hank McCoy, has a secret lying deep within him. This "beast" has been controlled through the use of a serum. This time, though, the serum failed.

Episode 19: Adrift
Scott is visiting his brother, Alex, in Hawaii. While surfing, Alex gets lost on the ocean and Scott goes to his rescue.

Episode 20: African Storm
Storm is being terrorized by an African witch-doctor, member of the tribe she was once considered a goddess. It's up to Evan to prove to his worth to his aunt, who was thinking about sending him back home.

Episode 21: Joyride
Lance joins the X-men to get closer to Kitty. However, he finds out that there's much more to being good than it looks, as some of the new recruits decide to take joyrides during the night.

Episode 22: On Angel's Wings
While trying to teach Amara how to control her powers, Jean becomes involved in a women's rights discussion with Scott. To prove themselves to people, Jean, Amara, Rogue, Kitty, and Tabitha decide to form the Bayville Sirens and use their powers to help others.

Episode 23: Walk on the Wild Side
S. H. I. E. L. D. (Strategic Hazard Intervention Espionage Logistics Directorate) has contacted Logan. They want him to retrieve a stolen machine, which was once used to create the legendary hero, Captain America. As Rogue and Nightcrawler come to his aid, more and more things are revealed about Logan's past.

Episode 24: Operation Rebirth
Mesmero, a circus hypnotist, uses his mutant powers to take control of Jean, Spyke, Shadowcat, and Nightcrawler and makes them steal three ancient Tibetian rings. As the X-men try to stop their friends, Mesmero escapes with the rings, which make up the first key that unleashes great evil.

Episode 25: Mindbender
Forge tries to help Nightcrawler by slowing down his teleportation and finding out more about it. As they learn that he passes through another dimension, Kurt learns that its habitants aren't exactly friendly.

Episode 26: Shadowdance
Beast is feeling a little trappeed and isolated. So, Kitty plans a field trip, as an Earth Sciences project, to the Redwood National Forest, where Beast is mistaken by the legendary Bigfoot.

Episode 27: Retreat
Beast is feeling a little trappeed and isolated. So, Kitty plans a field trip, as an Earth Sciences project, to the Redwood National Forest, where Beast is mistaken by the legendary Bigfoot.

Episode 28: The HeX Factor
Wanda Maximoff was locked away by her own father because she couldn't control her powers. As Xavier tries to help, an angry Mystique takes Wanda out of the Institution and instigates a battle against the X-men.

Episode 29: Day of Reckoning I
As Wolverine suddenly vanishes, Magneto decides that it's time for the world to know the wrath of mutants. Professor Xavier decides that the X-men alone are no match for Magneto and his team, so he recruits the help of the Brotherhood. The new recruits, along with Scott, are left having to fend for themselves.

Episode 30: Day of Reckoning II
A robot, the Sentinel, is being developed to stop mutants. As the X-men and the Brotherhood battle off Magneto and his recruits, Quicksilver decides it's time to side with his father. Meanwhile, Scott and the new recruits have a hard time trying to escape a kamikaze mansion.

Season 3

Episode 31: Day of Recovery
The world is a changed place now that mutants have been exposed. People fear going outside their houses, the country is on alert, even the X-men have to find a way of dealing with the news. With the Institute destroyed, the X-men split up. Some take shelter in the sewers, where they find more mutants, while others try to rescue the rest of the X-men, with a little help from Nick Fury. Is Mystique right? Can humans and mutants really learn to live together?

Episode 32: The Stuff of Heroes
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 before he further turns the public against mutants. Even Cyclops' unvisored energy blasts can't stop him, but they get his helmet off so Rogue can touch him and take his powers, defeating him and finding out from his thoughts where Professor X is - left in Juggernaut's old holding cell by Mystique. The President clears the X-Men of all charges, reveals that Trask was the one responsible for the Sentinel attack, and asks the public for understanding.

Episode 33: Mainstream
The X-kids are allowed to go back to school, but the pressure of mutant hatred poses to be too much for Kurt, who doesn't want to stand by his friends. Jean is invited to speak in behalf of mutants. Meanwhile, with information given by Principal Kelly who doesn't want mutants roaming around his school, Duncan confronts Scott and the other X-men (minus Kurt) in the parking lot. Scott stands up to him, but Duncan had asked the Brotherhood for help.

Episode 34: The Stuff of Villains
Wanda goes searching for pietro,she finds him at a diner and procedes to get him arrested in the assumption that Magneato will come bail him out. Meanwhile the brotherhood are expelled from school, much to lance's disgust. Also Gambit shows up at school, whit the sole purpose of getting the brotherhood to join magneto and bust pietro. although he first saves evan from being expelled by scaring two students who got him to use his powers. Rogue and Kitty follow Gambit and the brotherhood by their own way of hitch-hiking.They almost get captured by the army but are saved by an officer who knew they were not to blame for the "accident" that busted pietro, who immedialty with gambits help asserts himself as leader of the brotherhood.

Episode 35: Blind Alley
Mystique escapes Area 51 with one thing on her mind: vengeance against the person who locked her in there. She tricks Scott into going to Mexico and leaves him in the desert. Without his ruby sunglasses, he uses his skills and a lot of luck to get back to the Institute. The bond between Jean and Scott is the only thing that will save him from Mystique's deadly plans.

Episode 36: X-treme Measures
Evan's mutation is becoming more and more difficult to control, and so is his temper. He finally finds solace and acceptance in a most unlikely place -- but at what cost?

Episode 37: The Toad, The Witch And The Wardrobe
Still in search for her father, Wanda stumbles upon Pyro, who leads her to a ski resort. While at Amanda's parents' house, Kurt has trouble making his image inducer work; things only get worse when Toad shows up to steal Kurt's inducer and win Wanda's love. His plans go under when Magneto takes Wanda into his lair. Kurt and Toad go to rescue Wanda, but not before Magneto, with the help of Mastermind, wipe out Wanda's memories of a bad childhood and replaces it with happy ones.

Episode 38: Self Possessed
The numerous personalities Rogue has absorbed over the years now start waging war for dominance within her. The ordeal cements a bond between her and one of the other X-Men.

Episode 39: Under Lock & Key
The original five get together trying to stop Mesmero from getting another key that would bring back Apocalypse.

Episode 40: Cruise Control

Episode 41: X23

Episode 42: Dark Horizon Part One

Episode 43: Dark Horizon Part Two