- It was sad to see Rogue and Nightcrawler believe Mystique had died for them through Heroic Sacrifice, and later we see Mystique's still alive and runs away crying from her birth son and adoptive daughter.
- About said daughter, having Jean go inside Rogue's mind and heart after she gets her memories of Mystique and Ms. Marvel, having her lock Marvel's psyche away so Rogue doesn't go mad, seeing Rogue cry and beg forgiveness to Marvel as Jean does so and later the visit to the hospital... "Her name's Carol Danvers... we once were friends. *snif*" SNIFFFFF.
- Xavier and Juggernaut's common backstory was also very sad and well-done. Especially when Xavier finds out the truth about his long-dead stepfather Kurt Marko by scanning Juggernaut's mind and then commenting that to Beast ("She did love him... He only wanted her money..."), to which Beast sadly says "A father's sins...".
- Perhaps what's worst of all is after the memories all play out, Xavier is still quite affected by them. "I thought I was over this, but I was so young and it hurt so much."
- "Nightcrawler" was just beautifully done.
- The scene where Rogue tears up after seeing Wolverine praying out loud in the chapel made me weep.
- The "Proteus" 2-part episode. Once you realize that this rendition of Kevin/Proteus is more of a deeply unhinged and love-starved Psychopathic Manchild who only wants his Disappeared Dad to love him, you view everything that happened in a very sad light.
- The episode with Magneto, Quicksilver and Scarlet Witch discovering their fucked up familial bond, Pietro and Wanda Calling the Old Man Out before abandoning him, and Magneto's despair and sadness that neither Xavier nor Beast can help him with.
- Are you kidding? The season finale where Professer X almost dies. He has a heart wrenching final speech on his death bed and all the X men are there.
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.. [and your tears start there]
- In the episode "Repo-Man" Wolverine has a flashback of how he met Heather and James Hudson, recently escaped from the Weapon X complex he was a wild savage who Heather had to tranquillize before he could kill her husband, they took him to their home and when Wolverine woke up he saw Heather but he was still in a berserker rage and shredded his restraints then advanced on her with intention to kill her. She pleads to him to listen to her and this:
Heather: We mean you no harm...we only want to help you, you've got to listen to me...please
[Wolverine snarls with his arm shaking before he retracts his claws, grabs his head and kneels]
Wolverine: Why did they do this?
[he sobs while Heather kneels next to him and embraces him]
- In the episode "The Final Decision" Gambit angrily protests the apparent suicide mission to rescue Senator Kelly from the sentinels base. An injured Magneto emerges from the infirmiry to remark on how foolish the professor and the team is for continuing to pursue the dream. The professor simply asks his team "is he right?" One by one the X-Men decide to depart. Jubilee, most enthusiastic remarks leading to this exchange with Wolverine
Jubilee: What's anybody waiting for? He needs us!
Wolverine: Sit down kid, you're not goin'.
Jubilee: (in tears) I'm not a kid anymore! I'm one of you, one of the X-Men. And it means more to me than anything in the world!
Wolverine: Yeah, that's what it means to me too.
- Jubilee is then allowed to join the mission in a foolish yet poignant decision. By now the music has gotten terribly tragic. Rogue walks to the rest of the team while staring daggers at Gambit who angrily gives in and joins them too. As their jet takes off, Magneto watches from the ground with one last remark. "You're all fools! Heroic fools. The brave are always, the first to die." The X-Men musical score was underrated because it was perfect for moments like this. Every single time. The whole scene can be viewed here.
- One of the closing scenes for "Weapon X, Lies and Videotape"...it's just Wolverine sounded so old and tired while he despaired about what happened at the Weapon X complex and with good reason, that place is full of painful memories for him and it tormented him endlessly throughout this episode as he found out that most of what he remembered before he broke out of the complex was faked.
Wolverine: What does it mean Hank? I came here to find answers...now I know less than I did before...can't even trust my own memories
- However, the carving on the tree suggested that Wolverine and Silver Fox really were in love. But as she said, "that was another lifetime."
- Cyclops calling out Corsair. That's all.
- The exchange is pretty gut wrenching for a kid's show:
Corsair: Son, how can you believe—?
Cyclops: Don't ever call me that. For twenty years, I dreamed about my father - a man to look up to, a hero that sacrificed everything for the good of his family. It was your family you sacrificed! You threw us away so you could go knock around the galaxy!
Corsair: That's not what happened!
Cyclops: Oh?! Did I imagine the orphanage or the foster homes where nobody wanted me?! Tell me, 'Dad,' am I making this up?!
- The last five minutes of "Child Of Light". It's just so touching...
- Corsair explaining to Cyclops what happened to his mother in "The Starjammers." Thing is, at this time, neither knows the truth, so Corsair isn't being delicate. Later on, he mentions his children, "I remember my oldest boy. He had his mother's eyes."
- In "Nightcrawler," both Wolverine and Nightcrawler exchange their views on God. Viewers find that Wolverine used to believe, but lost his faith. ("What kind of God would let men do this to me?" extends claws) Nightcrawler tries to reassure him, but later by himself, he falls over and laments the hatred directed at him because of how he looks.
- "The Fate of Phoenix." Once it becomes clear that she can't contain the Dark Phoenix forever, Jean begs Cyclops to finish her:
Cyclops: Fight it, Jean! Use the powers of your mind!
Jean: I can't fight it, Scott - never every second of every day, not slipping not even for an instant! Scott, please, do it!
Cyclops: I... can't!
- Seeing that Scott was unwilling to finish her, Jean then sees no choice but to make a Heroic Sacrifice by energizing the Shi'ar Imperial ship's Wave Motion Gun, and runs from Scott before blasting him away, as the weapon is fired at her, ending her life.
Jean: I love you, Scott. Part of me will always be with you.
- Xavier senses that Jean had perished, and sorrowfully tells Lilandra "You've won.", but it's clear that no-one took any joy over what happened, and even Lilandra was in tears.
- "Beauty & The Beast." Poor Beast. He falls in love with a normal human, Carly, and vice-versa. But her father is bigoted against mutants. This episode hammers home how hard Beast has it, as he laments his mutancy endangering his family and now Carly. He is unfortunately proven correct when the Friends Of Humanity abduct her. Though Carly is saved and her father's views changed, Beast still sacrifices his happiness.
- One instance in the episode has Beast in his room looking at his old family photos while Jean walks inside having made sandwiches for him. Beast acts descends into uncharacteristic rage by throwing the photobook away, then holding another book, and throwing into the mirror, breaking it. He then cries to himself, with Jean trying to comfort him:
Jean: It's Carly, isn't it?
Jean: We must think of how our gifts can benefit the world.
Jean: Hank...I had no idea she meant that much to you.
Beast: It was so much easier when I was consumed with my work. I could pretend that what other people thought of me didn't matter.
- Gambit in "X-Ternally Yours" after having to deal with his past back home. "I am not assassin or thief. I am an X-Man, and I'm never comin' back."
- Anything related to Morph. Specially the episode dealing with his PTSD.
- Also, anything related to Proteus. Yeah, his backstory and powers were all bowdlerized, but it's still damn powerful stuff.
- The series's rendition of the Phoenix Saga. Where do we start?
- The one featuring Quicksilver, Scarlet Witch and Magneto. Even Beast and the Professor can't help feeling like shit for Magnus.
- The episode where Scott finds out that Corsair is his father — in the worst circumstances possible, as Corsair has been famed for a crime and Cyclops is among those tasked with capturing him. Complete with a heartfelt, heartbreaking Calling the Old Man Out moment where Cyclops bitterly lashes out at his father as he explains his Dark and Troubled Past.
- The Bad Future in the episode "Days of the Future Past" when Wolverine past the graves of his fallen comrades. The camera angle zooms towards Jubilee hits him the hardest.
- Made even worse by the fact that, given their date of death, it's implied that Jubilee—the youngest of the X-Men—was the first to be killed by the Sentinels.
- The entirety of "Graduation Day," from beginning to end. Special points to the series' final lines:
Jubilee: "Can he ever come back?"
Xavier: "Perhaps not in body, my children, but my spirit will remain among you, where it was always meant to be."
- The episode that revealed some of Rogue's origin, and showed how she gained her super strength and ability to fly: By absorbing too much of Ms. Marvel's powers she accidentally absorbed Carol Danvers' mind. For years Carol was trapped inside Rogue, becoming warped and twisted over Rogue stealing her life while her body lay comatose in an hospital. Combined with Rogue's guilt over this is that Professor X could only offer the option of sealing Carol away until they could figure out what to do, so that way Rogue wouldn't be driven insane by Carol nor be haunted by her guilt. (And as she takes it, Rogue is crying in Jean's arms and begging Carol to forgive her.) What's worse, the second time Carol has to be sealed involves Rogue being forced to take an active hand in the process. Though the end of the episode seems to imply that Rogue was able to transfer Carol's mind back into her comatose body.
"Her name, it's Carol Danvers. We used to be friends"
- In the episode of "Storm Front", Storm discovers that the ruler of an alien world, Arkon, who she fell in love with, isn't as noble as he made himself out to be, and is actually an oppressive tyrant who enslaves people to build the tower to control the atmosphere. Storm flies off in a rage angry at Arkon's deception and nearly destroys the capital. It's only Jubilee's words that calm her down and bring her to her senses. After freeing the slaves, the Arkon and his homeworld, destroying her statue and the tower (which also controls the slaves) before returning to Earth. The final scenes of the episode show she was clearly heartbroken over everything that occurred.