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Tear Jerker: Transformers Armada
All of Starscream's inner-thoughts in "Crisis", he didn't want to harm the earth, he didn't want to fight Optimus. By the end of the episode his former human friends were nearly wiped out and he's at least partially responsible for the death of Optimus... Looks like no matter which universe your in, it sucks to be Screamer.
Starscream's suicide-by-Megatron. It wasn't Dinobot levels of dramatic, but it was getting there. There last talk certainly helps bring on the water-works.
Starscream: None of that matters now. You must listen, do as Optimus says and join forces with the Autobots, or else every last one of us is doomed! Please sir... do it for me...
That wasn't even the most heartbreaking part. The worst part is when they inform the children, and seeing their individual reactions Especially Alexis. I BAWLED.
How about the way Starscream's Minicon partner Swindle (who Starscream ejected so he wouldn't share the same fate) reacted, he just stands their, in the silence and asks Optimus if there's any hope of Starscream being alive. It's the way he beeps that really hits you in the gut.
The truly touching thing was that Starscream was desperately trying to get Megatron to do the right thing, even if cost him his own life. He made a point how he remembers that a very long time ago he made an oath to Megatron and knows that he could never bring himself to break that oath by striking down Megatron.
Smokescreen getting shot with the Requiem Blaster. Mostly just cause it looked so damn painful, even if Red Alert rebuilt him next episode.
Also if only just because he keeps trying to fight, even with the tree trunk-sized hole blown through his stomach and the metal on his body actually melting.
Optimus Prime's death. (It's Optimus, of course he dies at least once.)
What got me with Optimus's death in Armada was Jetfire's reaction, the screams and then his discovery that all that was left of Optimus was his faithful Minicon holding his Matrix.
Sparkplug was what did it for me too. He didn't seem to know what was going on, just that he had to hold on to that thing.
Galvatron sending himself to his own demise, knowing that if he lived the war would continue and Unicron would arise again. This show's got a high body count, but they make every one count.
After the final battle with Unicron at the end of Armada, Optimus is alive, floating in space. He sees the Matrix floating nearby and thinks to himself that he isn't worthy of wielding it, much less of being a leader anymore.