Let's see. Ratchet ends up in another world, is targeted by the main villain because of what he is, learns about his race and that they were purged, allies with someone who later backstabs him (but in a different game), finds out what happened to his missing father, and after defeating the villain, loses someone who is very close to him. That's quite identical to TRON: Legacy, though Ratchet has more in common with Quorra than with Sam Flynn.
Moral Event Horizon: While all Cragmites are born far beyond this line, it's clear that Tachyon joins his race. But WHEN does he cross it? After finding out his heritage? After his purge on the very species who raised him? After taking over Polaris and ruling it under his Iron Fist? After he brings back his evil race? Or when Ratchet and Clank confront him on Fastoon?
That One Achievement: "Everybody Dance Now" requires you to make all characters in the game dance using the Groovitron. No progress on the Skill Point is tracked, the Groovitron only has three max ammo and its ammo is hard to find, there are lots of similar enemies that count individually, and this also includes bosses and NPCs that appear only once or twice and obscure ones like the six types of penguins created by the Transmorpher and the GrummelNet vendors. You can buy the infinite-ammo Golden Groovitron to help out, but it costs 2 million Raritanium.
That One Boss: Although Tools of Destruction only has three boss battles (excluding the minor ones with the Leviathans and large pirates), all of them will have a lot of HP and will not provide the player with needed ammunition, making these battles almost unwinnable if you run out of ammo.
Tachyon gets a special mention. While he is not too difficult, some of his attacks grant him Mercy Invincibility that can last for several seconds. It gets especially noticeable by using the RYNO on him. Combined with the aforementioned lack of ammo and health and the fight can get rather frustrating.
That One Level: Planet Viceron, aka, Zordoom Prison, especially during the "Escape from Zordoom" mission.