This is the only game in the franchise to have a Downer Ending, so heartretching moments are expected.
As a Moments subpage, all spoilers are unmarked as per policy. You Have Been Warned.
- Captain Slag's death. 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.
- 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, and even 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 Japanese version of this scene has Ratchet scream Clank's name a second time before he finally vanishes.
- 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.
- The lombaxes' fate. All they wanted was to give one unborn Cragmite a second chance, and show that they can be good if they're raised under love and care. Tragically, Tachyon found out about his heritage, grew to hate the lombaxes in spite of them sparing his life when miners found his egg, and plotted not only to bring his Always Chaotic Evil race back to destroy the universe, but plotted genocide against the lombaxes. Simply out of pure hatred.
- While many lombaxes were killed in the genocide, including Ratchet's mother, the survivors fled for another dimension in the hopes that Tachyon would leave the universe alone if he was to think that he succeeded in killing them all. This provided to be a tragic mistake, as Tachyon would proceed to turn Polaris into a fascist dictatorship and use his power to kill trillions in various offscreen genocides.
- There are some points throughout the game that implies that Tachyon was evil ever since he was a child, most likely even before he learned of the Awful Truth. This means that, for Cragmites regardless of how they were raised, evil was inherent. The lombaxes were doomed to be exterminated from the moment they decided to spare Tachyon, regardless of whether he ever found out about his heritage.
- We know what became of Ratchet's parents, and sadly, he never got a chance to know them. His mother died in the genocide, and his father, Kaden, just grabbed the boy and sent him to live in Veldin before his ship was blown up by Tachyon, who took great pleasure in the killing.
