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NT Warrior
- It's mentioned in the first episode that Lan's dad rarely comes home and that he hasn't been good about keeping his promises to his son, specifically one about when he would get his own Navi.
- Tory being blackmailed with his Dad's life by Maddy so she can take control of the Water Works.
- MegaMan getting deleted in episode 22, Taking the Bullet for ProtoMan when PharaohMan ambushes him. All Lan can do is stare blankly with tears streaming down even as the building comes down, clearly destroyed at what had happened. Thankfully, thanks to everyone’s efforts, MegaMan gets better but still.
- After the hit connects, there are flashes to the various people who were watching the match, such as Lan, Chaud, ProtoMan, and various audience members. The dub truly sells this moment by adding audio of everyone giving their own internal Big "NO!" to the moment.
- Lan's reaction when being evacuated. All he can do is stare blankly at his PET and mutter MegaMan's name over and over. This is followed up by his own audible Big "NO!" in the dub or a Skyward Scream in the original Japanese.
- Chaud's reaction when he is being evacuated on the same helicopter as Lan. All he can do is watch the stadium sink into the sea, solemnly saying that he never wanted things to go so far.
- Virtual Idol Aki get corrupted by a virus and attacks people dressed up as her because she operates on a different system and has no way of truly interacting with anyone outside of a screen, including other Navis.
- After a very realistic dream, Count Zap wakes up in the ruins of his old family home and laments that there was no way he was talking to his mother since she has been dead for ten years.
- To make matters worse, it was obvious that she favored her older son more.
- Despite being a Bratty Half-Pint, it's hard not to feel sorry for Yai when Gauss Magnets decides to shift around bank accounts and give her fortune to Higsby while leaving her family penniless.
- While comical, the CutMan Brothers are torn that their eldest brother was deleted down by MegaMan. They set off to avenge their brother, declaring that MegaMan is a menance to society, all without knowing that their brother was actually deleted because he was part of a criminal group.
- Princess Pride. She is a young teenager who dresses up as a boy sneaks away from her bodyguards to have fun while in DenTech because as the ruler of a nation that is constantly under attack by an enemy nation called Darkland, her life for the next five years is easily planned for her.
- The deletion of TorchMan. Unlike other NetNavis in the series, he doesn't have enough to rebuild himself completely.
- Sal finding out that her childhood friend Daisuke is the Nebula hacker she is hunting as Black Rose.
- Chaud watching as ProtoMan is deleted by the Gray Virus Beast, who crushes the Navi in his jaws.
- Bug Style MegaMan. After absorbing so much data he ends up in agonizing pain to the point he can only call out for Lan to help him.
- Dex's lies to his little brother Chisao. He lied about how his friends were all delinquents he set straight and now commands in order to impress his brother, a lie that the others have trouble swallowing but do so to help their friend.
- It's heavily implied that the boy's parents are divorced since Chisao lives with his mother in a completely different city. Then, it's revealed that Chisao is a protege when it comes to battling and goes to an elite school for genius kids. The snapping point for Dex hits when Chisao is able to perform a Program Advance with Gutsman, something even he was unable to do.
Axess
- While Lan was able to weakly respond to MegaMan after collapsing from using CrossFusion for the first time in the dub, the original cut of the episode had Lan passing out with MegaMan desperately begging him to wake up.
- Raika giving some food rations to Lan during one of their team up missions, stating that cheap rations were all that people could afford to eat in Sharo before the Rare Metal mine was discovered.
- Misaki watching as Lan is able to use CrossFusion, the experiment he failed in performing back in the beginning of the season.
- Misaki giving in and going with the fake Inspector Manuela, who is really Ms. Yuri in disguise, and using a Dark Synchro Chip.
- Despite being one of the main villains of the season, Shademan watches as his friends, the Darkloids slowly get corrupted by the dark chips to the point that they're just mindless husks who only want to get their hands on more Dark Aura to feed their addiction to it.
- MegaMan NT Warrior got much darker during the Axess season, and the episode "Mariko to Yuriko/Ms. Yuri's Mission". Though the Heroic Sacrifice at the ending is fairly predictable, what makes it all the sadder is that throughout the episodes, Yuri is receiving messages from Nebula that she will never be accepted by society again—and they're probably right. She spent the series seemingly as a monster, trying to kill civilians in many terrifying ways.
- Ms. Mari's Big "NO!" near the end of the episode as she has flashbacks to her childhood while overlooking the highway her sister and Agent Misaki fell from, realizing that she lost her little sister a second time in the dub. Only thing worse is the original version, where she screams her sister's name.
- In the dub, the ending narration from the news channels saying that they did not find Misaki or Yuri's bodies.
- Another (probably the most famous tearjerker of the NT Warrior series) moment would be when Lan is given the Sadistic Choice of ether using a Dark Chip on MegaMan, or not and letting himself and everyone with him die. MegaMan says he's okay with turning into a virus-infected Navi if it saves his friends. Chaud and ProtoMan take the chip and use it themselves.
- The worst part is it ends up being a mostly Senseless Sacrifice. ProtoMan does make a minor comeback against ShadeMan with it, but ShadeMan quickly overpowers him and Proto Soul (which probably would have been unlocked anyway because of the desperation of the situation) is what ends up saving the day.
- Bass destroying his creation Allegro because the latter grew too independent.
- A flashback note shows Chaud's mother died when he was just a toddler. His father immediately scolds him for crying at his mother's grave marker and tells him that he will begin training to take over the family company the next day and that a NetNavi has been picked out for him. The NetNavi in question? ProtoMan.
- Chaud's line in the dub after ProtoMan has been saved from the Dark Aura is that he needs a vacation. This is a bit of a tearjerker when you realize that Chaud is barely twelve years old and is Vice President of his family's multi billion dollar company, assist with police work as a NetSaver, and still goes to the an elite academy for schooling.
Stream
- Rei Saiko's NetNavi ShineMan keeps apologizing for failing to do well in a Navi Car Race. He is then reformatted and turned into Asteroid FlashMan while screaming.
- Jasmine and Meddy's backstory. Meddy belonged to Jasmine's best friend, who died from an illness. Not being able to look at her without remembering their child, the late friend's parents gave Meddy to Jasmine.
- Raika's friend Iriya acting cold to his while under the effects of Asteroid YamatoMan
- Fyrefox talking about his original NetNavi Nenjiro, who was deleted in an accident.
- Maylu's reaction to Lan and Jasmine having a bond as Duo's chosen ones and being able to see the comet, something regular humans cannot see.
- Dark MegaMan pretending to be the real MegaMan and begging Lan to delete him.
- Dark MegaMan urging his lighter half to go back to Lan as he attempts a Suicide Attack on Slur.
- The members of Neo WWW seeing their Asteroid Navis deleted in front of them. It was clear that they bonded with their partners, and the fact that their memories get erased of their time together is just heartbreaking.
- Earth is temporarily destroyed because Duo sees it as flawed, no thanks in part to Slur purposely reviving villains and giving most of them to those with evil intentions or those who are ignorant of the power they truly hold.
- Baryl and Colonel leaving with Duo via CrossFusion to travel the cosmos.
- In earlier episodes, there were scenes of an elderly man dying before being buried with full military honors. The man in question is revealed to be Baryl, thus completely a stable timeloop.
- A happy tearjerker, but Yuri and Mari are able to reunite with each other and stay as a family.
- Dr. Wily appears a few times during the season, as a homeless man living in a shanty house. After the previous season, it's safe to say he practically lost everything.
Beast
- Lan is able to meet with the Beyondard version of his grandfather Tadashi, only to realize he's a hologram/AI that can only be used once due to the projector being damaged.
- The fact that the Cybeasts are rampaging and the Beyonard world is all but a wasteland is because of Dr. Wily and his grudge against Tadashi's accomplishments. No matter the universe or timeline, it seems that the two old friends are always destined to be bitter enemies.
- Colonel temporarily being recruited into Gregar's army.
- Everyone saying their farewells to Iris and Trill, who must remain in their world to help rebuild it after the Cybeasts all but destroyed it.
- Double the tears go for Lan and MegaMan, who had raised Trill since he was first given to them as an infant program. They aren't just permanently parting with a friend, but their little brother.
Beast+
- When SearchMan is investigating a break in he attacks the suspects, only to react in horror to see that he attacked his friends. Thankfully, they were the enemy in disguise but still!
- Lan screaming as he is trapped by Cache. Even MegaMan feels that his friend has been captured and demands Cache to return him.
- The copy of Trill appearing to Lan and MegaMan in the final episode. Even if the world is restored, the version of Trill who came to save them was just a copy of cache data and a reminder that the original Trill can never come back.
