Moment pages never use spoiler tagging — so beware of unmarked spoilers
The ending of the season one finale has a number of such points, all conglomerating in one big Heartwarming Moment.
Most memorably the scene where the X-Men are deciding whether or not to rescue Senator Kelly.
Jubilee: What's anybody waiting for? He needs us! Wolverine: Sit down kid, you're not goin'. Jubilee: (through tears) I'm not a little kid anymore! I'm one of you, one of the X-Men, and it means more to me than anything else in the world! Wolverine: Yeah, that's what it means to me too.
After having been gone so long Rogue is worried, Gambit appears, exhausted but unhurt, behind Cyclops.
Gambit: I t'ink maybe you miss me, eh? Rogue: (covers his mouth with her hand and kisses the back of her hand) Ah hate you! (Hugs him) Gambit: I don' understan' dis woman.
Xavier, piloting the Blackbird, has been shot down and is about to crash...when suddenly the plane halts in midair. Magneto holds the plane casually aloft with his powers, laying waste to Sentinels with a gesture of his other hand.
Magneto: Did you think I'd let you die alone, Xavier?
Gambit and Rogue finally admitting how they feel in the finale of season two. Also a TearJerker, as both of them are depowered and in a highly dangerous situation, and Rogue is terrified. Gambit, himself weakened, can't protect her, and can only use the moment to kiss her and tell her he loves her before she's taken away.
The series finale. Magneto is poised to take control of a giant mutant army. The X-Men arrive and ask him to go to Charles since Magneto is the only one who can save him.
Jean Grey: How much do you love Charles Xavier? Magneto: How dare you ask me such a question! He was my only equal. I owe him my life! Jean Grey: What would you do if you knew you were the only one on Earth who could save his life? Magneto: Do not play games with me! Jean Grey: Listen to me. A telepathic message to Lilandra is Xavier's only hope. You may be able to supercharge his mind just like you did mine. His brainwaves are electromagnetic. Magneto: You lie to torture me. My legions await my command pledging body and soul to me. With a single word I can remake the world. I can not leave. Cyclops: You know what you should do. Magneto: Why now? My greatest enemy; and perhaps my only friend. But I have waited all my life for this moment! Cyclops: Wouldn't he do it for you? (Cut to Xavier's bedside) Xavier: Hello, Magnus. Surely you have more impressing business than nursing an old friend. Magneto: Nothing more important. Xavier: Thank you. It seems I have quite an audience. Thank you all. I'm grateful to have the chance, to say goodbye.
Then there's the scene just before Xavier leaves:
Xavier: Morph, it's nice to see you home. In facing your fears, you have proven yourself truly an X-Man. Gambit, how often must the scoundrel prove himself a hero, before he believes it himself? Jubilee; You are the future. When I look at your face, I see hope. Storm...my beautiful Storm. Mighty as a hurricane, gentle as a summer rain. You honor me with your friendship. Wolverine; Loner: you have found a family. Wild savage: you have found dignity. Cynic: you have found faith. Rogue; unable to touch, yet look around you. You will find that you have touched us all. Jean, first in my heart. Your courage allowed you to see things no other human ever has, yet remain the same innocent child I met so very long ago. (grimaces in pain) Beast: Is there anything I can do, Charles? Xavier: "The friends thou hast, and their adoption tried, grapple them to thy soul with hoops of steel." Xavier: Scott...were I your father, I would tell you that no truer son could ever be. I am proud, proud of you all, my X-Men.
Wolverine goes through the absolute worst day of his life, finding out that the little he does remember is fake. Silver Fox rejects him, saying that they never dated in real lifenote However, the carving on the tree suggest otherwise, but "that was another lifetime". The Weapon X base gets destroyed, eliminating any clues to his actual past. At the end of the episode, Wolverine laments that nothing he knew is real, but Beast says "I and the rest of the X-Men are real."
Wolverine: What does it all mean Hank? I came here to find answers, but now I know less than I did before...can't even trust my own memories. Beast: I have no simple solution for you Logan, but the X-Men and I are here for you now. Those are real memories... ones I know you can trust. Come on now... let's go home.
Speaking of Wolverine, even though it goes downhill for him later on the episode where he spends time with an Inuit tribe, just because he's so damn HAPPY for once, not brooding over Jean or his past or all the people who want him dead...he's finally just unreservedly happy. Then Sabertooth has to show up and screw it all up like the dick he is.
In "Repo-Man" after Heather and James Hudson found and tranquillized a savage Wolverine who had broken out of the Weapon X complex and was in a berserker-like state, they take him back to their cabin. Wolverine regains consciousness and attacks Heather again before breaking down in tears over what had happened to him. Heather embraces him while telling him it will be alright, in the months that followed Heather and James helped Wolverine adjust to civil life and restore his sanity.
Logan: "You've helped me...more than I can say."
James Hudson: "Believe me my friend, it was our pleasure."
From the same episode, the other members of Alpha Flight, upon learning they were duped and the government wasn't going to get Wolverine to join up with them again like they were told, immediately come storming into the lab to save Wolverine from the mad general who wants to vivisect him. They don't care that he left them for another team or they haven't seen him for years, he's still their friend.
Upon trying to get away, Wolverine nearly killed Hudson who tried to stop him from leaving them again. But Heather begged not to, for her. So he does, but with a warning to the rest of Alpha Flight to never find him again.
In "The Lotus and the Steel", Wolverine takes a 10-Minute Retirement from the X-Men to travel to Japan after his berserker rages nearly sets off while driving in a motorway. Jubilee, who was with him, feels responsible and hijacks one of the gliders to follow him. When Wolvie sees her again, he reassures her that none of it was her fault, and that he just needed to sort out his issues himself.
Rogue frequently laments how she can't touch anyone without killing them. Most of the X-Men have chosen not to acknowledge her self-pity, or to indulge it. Beast's response is to try to make her smile.
Beast: You were lucky. I had dandruff.
The Beast's relationship with his patient Carly has some heartwarming moments, such as when she quickly accepts his appearance after becoming able to see. Also, a signed picture of Carly is seen on the Beast's desk in a later episode, suggesting that the two of them kept in touch even after finding it too dangerous for them to have a romantic relationship.
It's her reaction to Beast being the first person she ever sees:
Carly: You're...beautiful Beast: So are you.
Then there's this exchange between Jean and Hank when he laments that the fact he is a mutant is preventing him from seeing Carly. Jean comforts him, and immediately could tell what was wrong without Hank mentioning a word (without even reading his mind), showing how close two of the first X-Men are to each other, and how tightly knit the X-Men are as a whole.
Jean: It's Carly, isn't it? Beast: Why did this happen to me? Why couldn't I be normal? It's not fair. Jean: We must think of how our gifts can help the world. Beast: Gifts? I can't be close around any human. I can't take the risk of endangering them. My parents, my brothers and sisters, and now — now the woman I love. Jean: Hank, I had no idea she meant this much to you. Beast: It was so much easier when I was consumed by my work. I could pretend that what people thought of me didn't matter. Jean: How does she feel about you? Beast: I think... that she cares about me. Jean: Hank, that's wonderful! Beast: No! I can't allow her to be with me! It's too dangerous. Jean: You have to let her decide to take that risk. Talk to her, Hank. Give her that chance.
A small one compared to the rest of that episode, but Carly's father getting over his hatred of mutants to thank Hank for saving his daughter, and restoring a bit of Beast's lost faith in humanity that things can change.
Wolverine and Nightcrawler have an intense debate about the existence of God. Wolverine's intense cynicism versus Nightcrawler's preaching beliefs. Wolverine doesn't appear to buy it. Then in the final moments of the episode he is seen praying very sincerely in a church. It's so heartwarming that Rogue tears up at the sight.
Nightcrawler overall seems to have made quite the impression on Logan. When he decides to fly off to Japan to get his head together, he remembers his example to Tame His Anger.
In "Till Death Do Us Part, Part 2," after Morph steals a minijet and flies off.
Wolverine: Morph, no! Come back! Beast: Let him go, Wolverine. Morph may be afraid of what he would do if he stayed with us. He must learn to deal with what he has become. Wolverine: He's my friend. He's the only one who could ever make me laugh. I'm not gonna desert him this time.
A small moment in "Juggernaut Returns," as Xavier summons the scattered team to deal with the current threat. We see that Cyclops and Wolverine were at Muir Island, visiting a recovering Morph. Jubilee in addition seems to have gone to visit her foster parents from the pilot.
And the ending, where Juggernaut decides to give up the fight.
Xavier: He chose not to continue his attack. I believe that is his way of saying thank you.
The climax of "Sanctuary, Part 2," where Xavier asks Magneto to return to Earth with him. Back on Earth:
Amelia: Why did you offer to save Magneto? Xavier: He is my friend. Nothing can ever change that.
After Storm has fallen unconscious from stopping Magneto's nuclear missiles, Wolverine actually calls Cyclops "buddy". A small moment, but given how the two usually interact, it's still worth noting.
There's also that Wolverine caught Storm as she was falling. Very minor qualification for Ship Tease, but it's worth noting that they are married in an alternate timeline.
A bit of an odd choice, perhaps, but Rogue's frantic concern over Gambit's safety in the "Sanctuary" two-parter shows how much she does care for him, despite their issues.
During a Despair Spot in the Phoenix Saga, when the team is certain death is imminent, Gambit pulls Rogue into his arms and says if they're about to die, he wants the two of them to die together, before going in to kiss her.
In "A Rogue's Tale," Rogue regains all of her memories from before she joined the X-Men—particularly being used by Mystique against Ms. Marvel. After absorbing Ms. Marvel's mind, she runs away from home.
Rogue:[narrating] And that's when he called out to me. Xavier: Mutant. Mutant. I feel your pain. Let me help you.
"X-Ternally Yours" hits Gambit pretty hard—ending with him severing all ties to Belle, his brother, and everything else he knew. As he sits on the mansion's steps all depressed, Rogue joins him. Rogue herself shows genuine concern and care for Gambit throughout the episode, even while he is absent. Responding with threats and angry barbs whenever he is mocked by Wolverine.
In "Love In Vain", Gambit's concern for Rogue throughout the episode is touching, especially given that she's considering leaving the X-Men (and him) to be with Cody and Gambit has more than a little Green-Eyed Monster going on. Once Rogue realizes what Cody has become, Gambit rescues her from the hivemind and continues to hold her afterwards to comfort her.
"Xavier Remembers" ends with Xavier realizing that the Shadow King's actually gave him a priceless gift:
"Yes, he forced me to think through why I formed the X-Men and why we fight for our ideals and for each other. In short, why I live. For that, I will always be grateful."
In the Whole Episode Flashback "Descent", detailing the origin of Mister Sinister, as dark as the episode was, we see one glimmer of hope when Dr. James Xavier one of the ancestors of Professor X, comes across one of Essex's mutant test subjects in a church: lonely, confused, and afraid, begging God for forgiveness believing that his abilities came from the Devil. It turns out that he was just a poor young man from Ireland who came for work after a famine, but he had the terrible luck to run into Dr. Essex. He understandably panics when Xavier announces he's a doctor himself, but Xavier insists he's nothing like Essex, and only wants to help him. Xavier confronts an angry mob and defends the man — saying while he is indeed different, he is as human as the rest of them. It's easy to see where Professor X's courage and compassion comes from.
In "The Phalanx Covenant, Part 2," Magneto is approached by the group to help save the world. However, he's depressed over the loss of Asteroid M and doesn't care what happens. He changes his tune when he says Quicksilver is among the Phalanx's victims.
When the crisis is over, Xavier is idealistic about mutants who previously wouldn't work together joining forces to save the world. Magneto is far more cynical—saying everyone only acted in self-interest.
Xavier: Even if you have given up hope for yourself, Magnus, there are reasons to work for a better future. Here comes one now. [Quicksilver walks up] Magneto: Pietro! Thank God you're safe. [hugs him]
A hobo (actually a de-powered Sauron) begs Wolverine for help. You'd expect Wolvie to brush him off rudely, but he actually reached for his wallet to give him some change.
Season 4's "Family Ties" saw the revelation that Wanda and Pietro Maximoff, the Avengers Scarlet Witch and Quicksilver, are the children of Magneto. The three are led into a trap in the graveyard where Magda, Magneto's wife is buried. The mutants get into a scrape with the High Evolutionary's "New Men", and when a stray blast knocks over Magda's headstone, the usually calm and collected Master of Magnetism lets out a primal cry of anguish and starts kicking all kinds of ass.
Wolverine as a Papa Wolf to Jubilee in general. Wolverine is a gruff, jaded, traumatized man, but he outright admits Jubilee has him wrapped around her little finger, and he's often caring, tender, and protective towards her even while antagonistic with other team members.
Rogue and Gambit's relationship is actually portrayed really sweetly throughout the series. Rogue's powers preclude them from ever seriously getting together, Gambit enjoys his Chivalrous Pervert shtick, and both are prone to isolating themselves out of self-loathing. But despite all that, they're repeatedly shown as very close and caring for each other very deeply. In any episode focusing on either one of them, the other one is shown either trying to talk them out of doing something reckless, frantically worrying about them, trying to save them, or just providing emotional support - even when it's a Romance Arc with someone else. The fact that their relationship is largely Out of Focus save for a handful of episodes, and much of this is portrayed more as a background detail in larger plots - and yet they still have so many moments listed on this page - makes the constancy of it even more heartwarming.
Senator Kelly's entire arc in the first season. He starts out as an outright bigot, wanting to round up mutants and put them in camps and championing the Sentinels. But when the X-Men save his life twice he comes to realize that mutants are just human beings and does a Heel–Face Turn. In the Season 2 premiere, when the Friends of Humanity stage a mutant attack, his first thought it to call out to the "mutant" that he just wants to help him.
His very first act is to pardon Beast.
"Beyond Good And Evil", the Series Fauxnale would have ended on a far more happier note.
Xavier and the psychics defeated Apocalypse for good this time. Sadly, Season 5 would undo that action.
Cyclops and Jean are finally going to have a happy life as husband and wife.
Professor X and Magneto are in better terms due to them working together stopping Apocalypse and a possibility the two will put down the hatchet in the future.
Cable of all people would be the one to end the series. Now that Apocalypse is no more, what does he do now? Go back to his own time and be with his son.
