Being an Alternate Continuity of the X Series, it has several Tear Jerker moments.
- All viral Maverick. Viral Mavericks do come as Jerkasses, but they actually are good persons, whether they were Nice Guys in the games or they are Adaptational Nice Guys; they're just Brainwashed and Crazy because of the virus. Even Sigma is under this.
- Alia after she's rescued by X from Chill Penguin. She blamed herself for her unit's death.
- She also was shocked when her trainer, Flame Stag, went Maverick.
- Even worse, until Flame Stag joined X's team, X couldn't bear himself to tell Alia about his plans.
- She also was shocked when her trainer, Flame Stag, went Maverick.
- The relationship between Cadis and Tripwire/Wire Sponge. When X first met Cadis, she was claiming she was a Maverick for no reason other than the fact her friends have died. She makes new friends among the Maverick Hunters, including Tripwire, who actually is the one who killed her friends.
- Even worse, Tripwire suffered of a Heroic BSoD after his Heel–Face Turn.
- The talk between Tripwire and Cadis after Double nearly kills the latter qualifies as such, while also being a Heartwarming Moment. Since the entire medbay was filled with cyborgs, Tripwire was forced to reveal that he actually is Wire Sponge. Cadis is, thankfully, very understanding, allowing Tripwire to finally break out of his Heroic BSoD.
- The life story of Depthcharge/Launch Octopus. Only one human liked him. An old man, who was working past retirement to support his granddaughter, Jessica. Said man died before Launch Octopus went Maverick, and between the man's death and Launch Octopus going Maverick, Launch Octopus used a fake identity to help Jessica. This mostly heartwarming and is only tearjerking because no other human saw how kind Launch Octopus truly is.
- Zero's death in Rise of Sigma. It's mostly as sad as it's game variation. However, unlike the game variation, this one crosses with Nightmare Fuel, as X goes utterly insane and kills Vile.
- After the Hunters arrest Bit, Byte and Vile, they refuse to become good. This obviously is sad for X, who believes there is good in everyone, just like his creator, Dr. Light.
- Repliforce. They were meant to fight for humanity, but because of the virus' manipulations, humanity turned against them. Just like the viral Mavericks, they either were Nice Guys in the games or Adaptational Nice Guys. What makes it more tearjerking is that General defies the Spared By Adaptation trope.X: "...I can save you, General."
General: "But I ask you not to. I have followed my ethics; let me die with them." - The cyborgs, especially if you look at their situation from the perspective of Shimmer/Sting Chameleon.
- IRIS, full stop.
- First, she nearly dies, which causes Zero to suffer a Heroic BSoD. This is similar to the game... except that in the game Iris is Killed Off for Real. Thankfully, X connects Iris to Zero's power core, saving her.
- The entire battle between Zero and Iris. Cyrex did a great job showing how much pain was Zero going through in the battle.
- The talk between Zero and Iris after the latter receives a new power core is both heartwarming and tearjerking. Both Zero and Iris are in so much pain because of their fight.
- Fridge Horror: When you consider Iris was created by GATE, whose creations were the victims of conspiracy, Iris becomes even more tragic: now that Iris is Spared By Adaptation, conspiratorial scientist would try to use the fight between Zero and Iris as an excuse to kill Iris. But the only way to do it is finding an excuse to label the Maverick Hunters as Mavericks, as Zero wouldn't let anyone hurt Iris, and the Hunters are supportive of Zero, who is the first Maverick to pull a Heel–Face Turn. It's even worse considering the fact there actually exist people IN REAL LIFE that hate Iris just because she fought Zero.