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Tear Jerker: Ratchet & Clank
Don't give me that look. This ordinarily snarky series took a turn for the emotional towards the end of A Crack In Time when Clank must stay behind at the Great Clock: "It is what I was built for." He holds his hand out to Ratchet, who simply kneels and hugs him close. The events that follow don't make you feel any better.
Azimuth: "Miserable heartless soulless little robot!"
Don't I know it— just thinking about "The Plumber's Advice" was enough to make me tear up for months after I finished the game. To those reading who haven't memorized the cutscene titles, "The Plumber's Advice" is the scene where Clank is in the Orvus chamber, after Ratchet's death, staring at the Great Clock's controls. Thought it's obvious that he wants to undo the aforementioned death, we hear one of Orvus's lectures ("The Clock is a gift-- and not to be tampered with") in the background, obviously keeping him from doing so.
Clank's tone of voice always stays fairly constant, regardless of his emotional state. When Ratchet's dead body tumbles over the ledge into emptiness, Clank screams his name. It is the only time in the entire series that he raises his voice above "polite, but firm".
Alister Azimuth's death
Captain Slag's death in Tools of Destruction. Although Played for Laughs at first, it would deeply affect Rusty Pete in Quest for Booty. Pete holds on to Captain Slag's head and talks to it like a puppet, telling it how the rest of the crew hate him and that Slag was his only real friend.
Ratchet willing to stay on the about-to-explode Dreadzone station so that he could save everyone else. And his exchange with Clank before the battle with Vox was touchy too.
Early on in Ratchet & Clank: Size Matters, on the last cutscene for Pokitaru, Ratchet snatches the Technomite artifact from Qwark's hand. Keep in mind that Qwark just wants to tag along after feeling sad that he doesn't know his real parents, and the look he gives after Ratchet says "Stay out of our way" is just heartwrenching.
Call me sentimental, one of Zogg's final lines in the comic series made me tear up. "I'm sorry, Ratchet. I truly am one of your greatest fans."
The ending of Tools of Destruction. Clank is snatched up by the now-visible Zoni while he's in a trance, and Ratchet is unable to catch him. He, Cronk, Zephyr, Talwyn, Qwark and Rusty Pete look on in sadness as the camera zooms out of the Apogee Space Station, bringing this cliffhanger down. Sure, the next two games resolve this trilogy, but DAMN did this ending hit it. If the sequels hadn't ever been released...
The music that accompanies that scene qualifies, as well. It's a Recurring Riff that also happens to be the very first thing you hear in the game. Where it was warm and inviting in the beginning, it seems so lonely and small at the end.
The fact that everybody in Apogee Station just walks over and looks at him stings, too— but not for the reason listed above. Given his usual attitude, you'd think that Ratchet would be one to fall squarely into Don't You Dare Pity Me!, but the protest never comes. The camera zooms out and we're hit with the music. It says a lot more than dialogue could have.
As silly as All 4 One happened to be, one of Ratchet's interactions with Susie (a young Tharpod girl) definitely qualifies. When she's trying to mount an attack on Ephemeris— which is the reason she's an orphan— Ratchet steps up and stops her.
The after-credits scene in All 4 One: Lawrence and Nefarious are traveling through space, and as Lawrence says that they can swing by to pick up Nefarious' weapons, the doctor looks over at a photograph taken of himself and the heroes, as well as Susie, and he looks like he's ready to shed some tears...
The cutscene Ratchet's Vision from Quest for Booty— particularly the first time you play though the trilogy.
The sad fact that Ratchet had NO friends before Clank met him.
Cronk and Zephyr's deaths in "Into the Nexus".
The reactions following were all the more heartwrenching, particularly Talwyn's when you consider that they were the only family she had after her father disappeared.