2. The X-Impulse
Sabertooth arrives in Bayville looking to cause trouble.  In Chicago fifthteen year old Kitty Pryde realizes she's able to walk through objects.  Confused she tried to forget about her abilities but a meeting with schoolmate Lance Alvers and an eventual proposal from Jean and Professor X makes it hard to ignore her gifts.  Deciding not to side with Lance and use her powers for profit the young girl accepts the Institutes proposal.
First Appearances: Kitty Pryde (Shadowcat), Lance Alvers (Avalanche)
Appearances By: Mystique, Sabertooth

3. Rogue Recruit
Professor X learns of a new mutant and travels to Mississippi to recruit the young mutant.  The mutant Rogue, who had no idea of about her powers, is terrified when she touches a class mate and ends up absorbing his memories and strength.  Disoriented and frightened from the experience and not being able to differentiate between her own memories and those of the boy she takes off.  Mystique works hard to undermine the X-Men in order to prevent Rogue from being recruited by taking the form of Wolverine, Storm, Scott and Jean and attacking the confused girl..
First Appearances: Rogue, Cody, Irene (Destiny)
Appearances By:  Mystique

4. Mutant Crush
When the X-Men try to recruit a new mutant they are beaten there by Mystique who enrolls the boy at Bayville High.  Fred Dukes' or the Blob can't stand to be laughed at and when Duncan runs into him in the hallway, he loses it.  Jean camls the mutant down and Blob develops a crush on her.  Later when she refuses to go with him he kidnaps her.  Scott and Rogue are drama partners, and when Rogue learns Jean is in trouble she comes to the X-Men's rescue.
First Appearances:  Terran, Fred Dukes (Blob)
Appearances By:  Mystique, Duncan

5. Speed and Spyke
While taking in her nephew's basketball game she discovers he has inherited the X gene.  When he gets arrested for breaking into the school and destroying property he finally agrees to move to the Institute.  Mystique visits Spyke's rival, Quicksilver and he's more then egar to cause a little trouble.  When Evan sets off to deal with Quicksilver on his own, the X-Men teach him he doesn't have to do it alone any longer.
First Appearances: Evan Daniels (Spyke), Pietro Maximoff (Quicksilver)
Appearances By:  Mystique, Magneto, Lance, Fred, Todd

6. Middleverse
After an argument with Scott over if they should attend Duncan Matthews party, Kurt teleports away to a long last lab.  His presence causes the security system to start self destructing. When Rogue enters she trips the security trapping Kurt in another dimension where Kurt meets up with Forge, a genius mutant who had been trapped in the dimension since the 1970s.  Toad finds the device that can help Kurt get back home but uses it to make things disappear as the X-Men try to find their missing friend and Rogue tried to deal with her role in the Brotherhood.
First Appearances: Forge
Appearances By:  Todd, Lance, Fred, Mystique

7. Turn of the Rogue
On a field trip with Bayville High Scott tries to be cordial to Rogue who still doesn't trust him or the other X-Men.  It's not until Mystique shows up and tried to harm Scott does Rogue realize she has been trusting the wrong people all along.  She protects Scott and eventually ends up saving his life and instrumental in their rescue by the X-Men.
Appearances By:  Mystique

8. SpykeCam
In order to get some extra credit Spyke sets out to make a documentary about elements in his life.  When Sabertooth arrives at the school once again looking for trouble he takes a special interest in Spykes project.
Appearances By: Brotherhood of Mutants, Sabertooth

9. Survival of the Fittest
When the X-Men are away learning mutant survival training, Juggernaut escapes from his prison with some help from Mystique.  Her plan is to steal the mutant locating device known as Cerbero, but Juggernaut is more interested in exacting revenge against his brother Professor X.
First Appearances: Cain Marko (Juggernaut)
Appearances By:  Mystique, Brotherhood of Mutants

10. Shadowed Past
Rogue continues to have strange nightmares which she realizes is somehow tied to Kurt.  She, Kurt and the rest of the X-Men learn that Mystique is Kurt's mother and that Magneto was somehow involved in what possibly happened to Kurt.  When Mystique tries to meet with Kurt alone the Brotherhood show up and attack him.  The rest of the X-Men show up and they take care of the Brotherhood but Mystique escapes never revealing what she had planned to tell Kurt.
Appearances By: Mystique, Magneto, Brotherhood of Mutants

11. Grim Reminder
Kitty tried to find some alone time in order to write her folks a letter, but a news report from Canada that sends Logan into a tailspin, and bad timing cause both Kitty and Kurt to be trapped on the blackbird with an out of control Wolverine as he goes in search of answers.  On their arrival a chip that had laid dormant in Logan's head is activated and Kitty and Kurt must defend themselves from Sabertooth and their fellow X-Men.  Finally Kitty is able to get through to Logan and all ends well.
Appearances By:  Sabertooth
 
12. The Cauldron (Part 1)
Scott learns that his brother is in fact alive and goes with Professor X to find him.  Along the way Professor X is kidnapped by Magneto. Each of the Brotherhood, along with Sabertooth square off with a member of the X-Men and the winners are taken to Magento's sanctuary in space.  Alex and Scott bond and decide to freely join Magneto.
First Appearances: Alex Summers (Havoc)
Appearances By: Brotherhood of Mutants, Sabertooth, Magneto

13. The Cauldron (Part 2)
 Professor X is shocked to learn Scott and Alex have joined Magneto and watches as Magneto displays his machine that execrates mutation to it's fullest potential.  Sabertooth is the first demonstration, then Scott and Alex but as they enter the machine Scott has seconds thoughts, but it's two late.  As the captured X-Men look on in horror Scott and Alex emerge aged and with white hair.  When the other X-Men approach the Summer's shoot it down causing chaos on Asteroid M.  In the tussle Mystique and Magneto get tossed into the machine, then Jean tries to convince Scott to leave Asteroid M with the rest of the X-Men.  As the asteroid blows up two probes escape, presumably belonging containing Mystique and Magneto.
Appearances By: Brotherhood of Mutants, Sabertooth, Magneto

15. Bada-Bing Bada-Boom (2)
Tabitha and Kurt get grounded for goofing off during a training session, causing them to miss the carnival.  Soon her father shows up asking her to do him a favor, steal the nights earnings from the carnival.  Jean and Duncan go to the carnival together and Scott spends some time with Taryn.  Tabitha convinces Kurt to transport them over, and end up having a great time, but Kurt remains concerned about getting caught.  However things quickly change when her father shows up again insisting Tabitha help him out.  Tabitha leaves the X-Men and takes up with the Brotherhood.
Appearances By: The Brotherhood, Bobby Drake (Iceman) , Tabitha (Boom Boom) , Wolfspane, Besurker, Multiple, Sunspot, Magma, Canonball, Jubilee, Duncan, Taryn.

16. Power Surge (3)
Jean's mutant powers begin to get increasingly stronger in bursts but she thinks or hopes that she is able to handle them.  Eventually she loses control and it is up to the X-Men to save her from ripping apart the whole mansion.  Rogue and Scott are instrumental in this and it appears Rogue still has some old feelings for Scott.
Jean's abilities start growing in sudden bursts. At first she tries to ignore it, but with each burst she has increasing trouble regaining control. Meanwhile the school gets a new science/phys. ed. teacher.  Introduces Hank McCoy Scott and Jean grow closer in this episode, foreshadowing their future relationship (which is constant through every incarnation of X-Men, televised or comic). As an interesting parallel, Rogue still hasn't gotten over her crush on Scott.
First Appearances: Dr. Hank McCoy
Appearances By:  Principal Kelly

17. Fun and Games (4)
When Juggernaut's stasis field malfunctions Professor X must leave to investigate the cause. Without any adult supervision the new X-Men decide it's time to have a party.  Jean and Scott are left in the middle of know where because the younger kids think they won't go for a party.  At the party Arcade gains access to Cerebro thinking it is just an enhanced computer and Mystique posing as Misty Willed downloads it's information.
Appearances By: Mystique/Misty
First Appearances: Arcade
 
18. Beast of Bayville (5)
When a normally calm teacher at Bayville suddenly starts having fits of rage the kids from the Institute begin to get worried.  Things get worse as hank gives into his rage and it is up to Spyke to save the day.
Appearances By: Hank McCoy (Beast)

19. Adrift (6)
While Scott is visiting his brother a storm sweeps up causing Alex to become disorientated at sea.  Scott steals a boat to find rescue him but he boat ends up over turning.  At the institute the X-Men learn that Scott is in trouble and head out to help him.  The search and rescue helicopter sent to pick up the two boys ends up crashing, and the cutter is unable to find the two Summer's kids, leaving the job to the rest of the X-Men.
Appearances By: Hank McCoy (Beast), Alex Summers

20. African Storm (7)
Storm contemplates sending Evan back home to his parents because he's not taking his role with the X-Men seriously.  However when a witch doctor from Africa comes to the United States intent on stealing Storm's power, Evan and the rest of the X-Men must come to her rescue.

21. Joyride (8)
Lance leaves the brotherhood to join the X-Men but finds his new teammates are having a hard time trusting him.  When various X vehicles start to get trashed, Scott and some of the other X-Men put the blame on Lance not releasing the culprits were the new mutants.  One night the New Mutants knock on Lance's door telling him they are going out for another adventure and ask him if he wants to come along since he's going to get the blame anyway.  He refuses but quickly realizes their planning on taking the X-Jet out and runs to get Kitty.  They phase into the Jet as it is taking off to stop Bobby, Jubilee, and Cannonball but during the flight Jubilee accidentally fries some of the equipment making the jet harder to control.  When air force jets tail them the young mutants mistakenly make hostile actions against them and Kitty must phase the entire jet through a mountain to secure their get away.  When they get back to the Institute Lance is blamed until the New mutants admit it's their fault.  Lance decides being an X-Men isn't for him and returns to the brotherhood.
Appearances By: Lance, Jubilee, Bobby, Jamie, Cannonball

22. On Angel's Wings (9)
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.  Introduces the Angel Kitty is shown lighting a Menorah in the ending montage, establishing that she is Jewish. Though Scott invites Warren to join the X-Men, Warren turns them down. In comic canon, Angel was one of the original five members of the team.

23. Mindbender (10)
After several nightmares Jean disappears.  Professor X is finally able to locate her in Boston stealing a ancient Tibetan ring from a home in Boston by using Cerebro, but by the time the X-Men are ready to deploy she is on the move again.  Jean later shows up at the Institute and recruits some of her teammates to join her through the same mind manipulation she is suffering from.  The climax occurs at a circus/carvinal where Mesmero is located.  A battle ensues that pits X-Men against X-Men but the end result is Mesmero gets away and opens one of the doors that appear to be imprisoning Apocalypse.
First Appearances: Mesmero, Apocalypse

24. Shadow Dance (11)
Forge invents a machine that slows down Kurt's teleportion in order to find out what happens during the process in hopes of increasing his teleports range.  In the first test everything works fine but a camera picks up shadowy monster in the horrifying dimension Kurt passes through when he teleports.  Logan accompanies Kurt the next time through and they almost don't make it out of the dimension after they are attacked by several the the monsters.  Kurt refuses to ever teleport again, and soem wonder if the monsters can make it into this dimesnsion.  Forge say the only way that would happen would be if one of Kurt's portal would be left open.  in the meantime the Sadie Hawkins dance is rapidly approaching and everyone is wondering who is going to ask who.  Kitty suggest Rogue wants to ask Scott and Jean tells Kitty that Duncan assumes she's going to ask him but she may have other plans.  Kitty asks Lance who initially tells her he'll have to think about it then tells her yes.  His excitements causes an unintentional tremor which amuses Kitty.  Kurt who had been liking a girl in one of his classes, Amanda is excited when she asks him to the dance.  Just when it appears Jean is about to ask Scott to the dance Taryn beats her and essentially Rogue to it. Rogue and Misty go without dates and when the shadow monsters show up everything goes nuts.  Amanda confesses to Kurt she knows the truth about him and it doesn't matter, and then urges Kurt to teleport them out of danger, which he does.  The rest of the X-Men, with some help from the brotherhood round up the troublesome monsters and send them back where they came from.  Amanda asks Kurt to show her his true self and he's pleasantly surprised when she doesn't freak out.
Appearances By: Lance, Duncan, Tabitha, Quicksilver, Blob, Toad, Taryn, Mystique/Misty
First Appearances: Amanda

25. Retreat (12)
Beast takes five of the students on a camping trip where he seems to be a bit down.  Some hunters spot Beast and figure he is Bigfoot and decided to capture him.  The students become worried when they can't find their teacher, who has been captured.  They rescue their teacher and take care of the meddlesome hunters.
Appearances By: Rahne Sinclair, Roberto, Bobby, Beast

26. Walk on the Wild Side (13)
During a training session Jean and Amara get angry when Scott interferes in their training session which makes them think that boys think they are better than the girls.  At school Amara confesses to Tabitha that she feels like Jean is pushing her too hard, so Tabitha invites her to go shopping after school.  After school Jean spots the two taking off in Lance's jeep chases after them in Scott's car.  Tabitha and Amara spot a car jacking and chase the culprits down followed closely by Jean.  Feeling empowered by capturing the car jackers, the three recruit Rogue and Kitty and form what becomes known as the Bayville Sirens.  They go around town stopping and solving crimes for quite a while until they get mixed up with a group of criminals who expected their arrival.  things take longer than necessary and they are caught by a cop.  The cop lets them go but warns them to stop or next time they won't get off so lucky.  Outside the cop turns out to by Mystique.
Appearances By: Amara, Tabitha, Mystique

27. Operation: Rebirth (14)
Magento returns and steals all the remaining information on a top secret project called Rebirth that Logan had apparently shut down way back in World War 2
Appearances By: Magento
First Appearances: Captain America

28. The HeX Factor (15)
Mystique returns to the Brotherhood with Wanda Maximoff, Magneto's daughter and Pietro's sister.  Mystique sets a plan in motion that will have her new and improved Brotherhood battle the X-Men.  During the battle Wanda almost single-handedly forces the X-Men to retreat.  As well Tabitha leaves the brotherhood.
Appearances By: Mystique, Tabitha, Quicksilver, Lance, Toad, Blob
First Appearances: Wanda Maximoff

29. Day Of Reckoning (Part 1) (16)
When Wolverine vanishes the Brotherhood joins forces with the X-men to take on Magneto. After they take off leaving the new recruits new behind the institute goes into self-destruct mode. Amara almost doesn't make it out but thankfully Tabitha is there to help her.  The two young mutants track down Scott who had stayed behind to get out the rest of the recruits.  When they get back inside they realize they only have ten seconds before the mansion explodes.
Appearances By: Amara, Tabitha, Mystique, Tabitha, Quicksilver, Lance, Toad, Blob, Magento
First Appearances: Bolivar Trask, Sentials, Remy LeBeau (Gambit), Pyro, Peter Raspuitin (Collossus)

30. Day Of Reckoning (2) (20)
Brotherhood/X-men find Magneto but are shocked to learn Quicksilver is on Magneto's side. A battle begins and suddenly a  sentinel is released.  Some of the X-men are trapped and those that aren't return to the destroyed institute.  Scott and the recuits explains what happened and then accuses Professor Xavier of blowing the institute up.  Professor X turns into Mystique.
Appearances By: Amara, Tabitha, Mystique, Tabitha, Quicksilver, Lance, Toad, Blob, Magento, Gambit, Pyro, Collossus, Principal Kelly, Taryn, Duncan, Amanda

32. The Stuff of Heroes (2)
Rogue and Wolverine avoid a group of soldiers when an alert goes out against mutants.  Storm and Hank meet with Congress to defend themselves.  Juggernaut starts making trouble and the X-men decide to take him down so the publics opinion on mutants isn't further tarnished.  When Rogue touches Cain she stops him and manages to learn where Professor X is at well.  The X-Men are cleared by the President and it is learned that Trask was responsible for the Sentinel.
Appearances By: Ice-Man, Beast, Juggernaut

33. Mainstream (3)
Construction of a new Institute begins as the older students attend a hearing to determine if they will be allowed to continue on at the school.  Since Kurt isn't recognized by anyone because of his hologram projector  he avoids being included in the hearings which causes some strain with he other X-Men.  Logan takes on Colossus and Principal Kelly tries to get members of the brotherhood to go after the X-Men and Duncan.  Despite the fight the board votes to allow the X-Men to return to the school.  Colossus indicates that Magneto may have something over him.
Appearances By: Ice-Man, Principal Kelly, Toad, Avalanche, Blob, Colossus

34. The Stuff of Villains (4)
Wanda looks Pietro and finds him at a diner and proceeds to get him arrested.   The Brotherhood are expelled from school. Gambit shows up wanting the Brotherhood to join Magneto and get Quicksilver out of jail.  Rogue and Kitty try to follow but are almost captured by the Army but one of the solider recognizes the two young women were not responsible for Quicksilver getting away.
Appearances By: Caliban, Scarlet Witch, Toad, Quicksilver, Avalanche, Blob, Gambit

35. Blind Alley (5)
Mystique escapes with a mission to repay Scott for leaving her behind.  She turns into Alex and lures Scott into a trap leaving him in the desert without his glasses or visor.  Jean senses Scott is in trouble as he is rescued from a pack of wolves by a group of oil riggers who he is forced to abandoned shortly after.  Jean and Professor X try desperately to pin point his location as Mystique tries to trap him again.  However Scott knocks out the lights in the building putting them on even terms.  Jean saves him and they admit some feelings for each other.
Appearances By: Mystique

36. X-Treme Measures (6)
During a skate boarding competition the sponsoring company is sabotaged by a group of mutants as Evan's powers continue to evolve beyond his control.  He is warned not to drink  Powr8 but doesn't heed the advice resulting in a bad reaction.  The mutants take him and go underground where he learns that Powr8 is poisons to mutants and that Powr8 has been dumping waste into the mutants sewers.  Evan chooses to stay with the new group of mutants.
Appearances By: Morlocks

37. The Toad, The Witch and The Wardrobe (7)
Wanda gets a clue from Pyro pointing her to a sky resort. Kurt meets Amanda's parents for the first time but Toad believes he can use Kurt's hologram projector to make himself more appealing to Wanda and goes out to try and snatch it from Kurt.  After Amanda's parents house is wrecked and the projector is taken Toad convinces Kurt to help him rescue Wanda from Magento.   The rescue goes well but Magneto employs Mastermind to wipe Wanda's memories of her horrible childhood from her mind.
Appearances By: Amanda, Scarlet Witch, Toad, Pyro, Magneto, Quicksilver, Blob, Avalanche, Mastermind

38. Self Possessed (8)
Rogue struggles to retain control over her mutant powers as the the traits of all those she had touched start invading her mind and body.  Mystique returns as Misty to help and goes with Rogue to a concert.  But the cramped conditions caused Rogue to touch several of the people that were around her including Misty.  Rogue unable to control her transformations takes on Sabertooth powers and goes wild.  The X-Men attack not knowing the person they are after is Rogue.  She is able to get away but is soon found by Mystique who tells Rogue she had adopted her.  Wolverine, Professor X and Jamie are able to figure out it's Rogue and help her as Destiny predicts the rise of a dark mutant power.
Appearances By: Risty/Mystique, Jamie, Destiny

39. Under Lock & Key (9)
Mesmero makes Gambit steal half of the Spider Stone from Angel but then is captured by Magneto. Magneto learns of the three keys and that they can free Apocalypse and follows Mesmero to London. Angel goes to the X-Men for help and they also head London. A fight ensues but Magneto manages to find the two halves and joins them, which create a energy spider. The X-Men try to get it while Magneto's team try to destroy it.  Xavier explains that Mesmero wanted Magneto to destroy it all along as it was the only way to stop what is coming.  
Appearances By: Angel, Beast, Ice-Man, Mesmero, Gambit, Magneto, Mastermind, Colossus, Sabertooth, Pyro

40. Cruise Control (10)

41. X23 (11)

42. Dark Horizon (Part One) (12)

43. Dark Horizon (Part Two) (13)