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).
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.
Even Mewtwo, of all characters, is affected by it; after spending his whole life believing that Humans Are the Real Monsters, seeing one trying to stop the fight is enough to bring some sanity into him.
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 Magical Defibrillator, 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 Please Wake Up.
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.
Despite the slight Narm of the scene, (and the song "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 There Can Only Be One fight to the death in the process.
JAMES: Now I know how terrible fighting really is.