There are cut quotes from Alister Azimuth in the game's main sound bank.
These include: Going on a secret outskirts mission with Ratchet's father, Kaden, in the Orrack Minor.
Kaden winning the Agorian Battleplex.
Kaden dating Ratchet's mother in Vapedia.
Seeing Lorna Cross, a relative of Angela Cross.

When the game was brought to Japan for localization, Ratchet's appearance was slightly altered to have bigger black eyebrows instead of the smaller brown eyebrows in the original, and has more shine added to his eyes.

In the cutscene involving the Plumber and Clank inside Clank's memory banks, the Plumber is trying to find a clog inside a large green pipe. When he tells Clank to jump in the pipe, Clank asks if the Plumber's coming too, to which he replies,"Plumbers don't just go diving down strange pipes all willy-nilly, that'd be ridiculous!" This statement, along with the green pipe, is a reference to the Mario Bros. series, and his affinity for using pipes for transportation.

The developers of the game held a contest for the fans to design a weapon for the game called "My Blaster Runs Hot". The winner was Spiral of Death.