Rodney Copperbottom is a young robot inventor who dreams of making the world a better place, until the evil Ratchet takes over Bigweld Industries. Now, Rodney's dreams – and those of his friends – are in danger of becoming obsolete.

Edward Wilson, the only witness to his father's suicide and member of the Skull and Bones Society while a student at Yale, is a morally upright young man who values honor and discretion, qualities that help him to be recruited for a career in the newly founded OSS. His dedication to his work does not come without a price though, leading him to sacrifice his ideals and eventually his family.

Scrat comes across a time machine and is transported to various times all in pursuit of his beloved acorn.