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Tear Jerker: Spider-Man: The Animated Series
After finally being freed from his imprisonment outside of the normal spacetime, Captain America willingly traps himself and the Red Skull again. And this time, there may be no way to free him again...
Eddie Brock getting sucked into a black hole like vortex, just after saving the only person he's ever cared about more than himself, ouch...
The death of Mary Jane's clone is pretty heart-wrenching, as is Spidey's Big "NO!" that follows it.
This also makes it the SECOND time that Spider-Man watches her die. The first one's heartbreak doesn't have time to set in before the Nightmare Fuel of Spider-Man legitimately ready to kill the Green Goblin.
Spider-Carnage's talk with the still-alive Uncle Ben from another reality to talk Spider-Carnage out of it. The speech moves him so much he actually starts crying, and subsequently performs a Heroic Sacrifice after realizing the Carnage symbiote still won't let him go.