The film's twist is that the World Grand Prix, run to promote a new alternative fuel, is a trap. A group of villains, a gang of 'lemon' cars led by Professor Z, uses a weapon disguised as a camera to make racers crash, discrediting alternative energy so that oil interests profit. Finn McMissile fakes his own death early on, and Mater is mistaken for an American spy. Mater's seemingly silly observations, such as the fact that Mater's own old parts and the villains' device look alike, help uncover the plot. The film ends with Mater and McQueen reconciled, with Finn's spy jet winking at Mater as he flies off.
Beyond the plot, the film's hidden meaning is that Mater's 'flaws' are his strengths, and that McQueen's real victory is regaining his friend's trust.