* If you've ever seen the short, then it's absolutely gut-wrenching for Mewtwo to lose his only human companion (who was a clone of Dr. Fuji's daughter), what makes this tragic is that he lost his memories of her right after she dies.
** After Dr. Fuji's stupid moment when he tells Mewtwo he's an experiment, Mewtwo destroyed the lab in his ''very'' pissed off moment. Not only does it appear that he's killed all of the scientists in the lab, but he also destroyed what's left of Amber/Ai (but after what he said, at least he's with his daughter now).
--> '''Dr. Fuji''': [[MyGodWhatHaveIDone We dreamed of creating the worlds strongest Pokemon, and we succeeded...]]
** On a related note, Mewtwo apparently ''killed'' people! [[WhatDoYouMeanItsForKids That's something horrifying in and of itself.]]
* Meowth's clone telling Meowth that they don't have to fight. They have a lot in common: the same earth, the same air, the same sky. If they could look at what's the same instead of what's different... well, who knows.
* Ash's petrification and Pikachu crying over his petrified body along with the rest of the fighters, clones included.
** Hell, ''[[EvenEvilHasStandards even Team Rocket]]'' are stunned by it.
*** Even ''[[BigBad Mewtwo]]'', of all characters, is affected by it; after spending his whole life believing that HumansAreTheRealMonsters, seeing one trying to stop the fight is enough to bring some sanity into him.
*** It also ultimately kickstarts his HeelFaceTurn, as he realizes that humans can't all be evil if one was willing to give his life for the safety of others, most of whom were either clones or Pokemon Ash had never met before coming to Mewtwo's challenge.
*** The music score "Tears of Life" during the scene is what really hits it home.
** Pikachu doesn't start crying until he realizes that even though he's a MagicalDefibrillator, his Thundershocks do absolutely nothing about petrification. He still kept shocking Ash, desperately trying to revive him, even though his Thundershocks were doing nothing. There's a good reason that Pikachu crying supplies the page image for the Tearjerker page under the Pokemon franchise.
** After Ash turns to stone, Pikachu gently shakes him and says "Pi-ka" as if asking him PleaseWakeUp.
*** In the Japanese version, the implications are even worse--Pikachu's "Pika-Pi" there was meant to mean "Satoshi" (Ash's Japanese name). Pikachu was repeatedly calling his seemingly deceased friend's name.
** Pikachu hits Ash over and over with electricity in an attempt to revive him, and continues until he simply can't produce any more electricity. His last attempt to shock him back to life doesn't even reach him, he's so drained.
** Misty's voice practically ''breaking'' when she faintly utters "Please, no..." as they all realize the worst has happened.
*** At the same, Brock's ''dead silence'' throughout. Remember that Brock spent most of his life in a PromotionToParent and it's highly unlikely that the resulting mind set went away when he started traveling with the much younger Ash (10 to Brock's 15). Add in the fact that Brock didn't stop Ash from running into the blast zone ([[{{Determinator}} Not that he could have]] but still) and it's clear Brock just essentially saw his little brother die in front of him.
* Pikachu just standing there taking hits from his clone refusing to fight is pretty heartwrenching too. The clone gets more desperate for Pikachu to fight back or fall down...only Pikachu to keep coming as it does neither, and he catches his clone when it drops from exhaustion.
** Additionally, the clone Pikachu actually starts crying in frustration as he slaps Ash's Pikachu again and again. Tears are still visible in his eyes when he collapses in the original's arms.
*** You don't even need subtitles to hear the clone going "Fight back!" with each slap and Pikachu's quiet and gentle but still firm "I won't".
** Despite the slight {{Narm}} of the scene, (and the song [[AwardBaitSong "Brother My Brother"]]) watching the two groups of Pokémon practically ''killing'' each other to prove which deserved to live was way different from watching a normal match between pokémon. The whole thing was pretty brutal.
*** It led to Jessie and James seeing the horror of a ThereCanOnlyBeOne fight to the death in the process.
----> '''JAMES:''' Now I know how ''terrible'' fighting really is.
*** In the exchange that follows, Jessie and James tearfully resolve to never fight with each other again. Doubles as a somewhat funny heartwarming moment.
* Pikachu's attempt at escaping Mewtwo's Pokeballs. His sheer terror and fear at escaping from something he fears a lot is pretty frightening to witness.