The game starts with the player choosing between playing as Autobots or Decepticons and deals with a story where the Decepticon Shockwave becomes all-powerful and ends up destroying Cybertron after obtaining the Zel Quartz, resulting in Rodimus Prime, Kup and Arcee going back in time to help the Autobots find the Zel Quartz before Shockwave does as well as Galvatron, Cyclonus and Scourge doing the same for the Decepticons.
- And I Must Scream: After taking the Zel Quartz for himself in the game's ending, Starscream ends up drifting in space forever because he runs out of fuel and the Zel Quartz loses its power when leaving its planet's surface.
- Big "NO!": Starscream shouts one in the final scene of the game, when he is left drifting through space without power after the Zel Quart loses its power.
- Dual Boss: There are some boss fights where you're fighting two opponents at once, most notably the final boss fight, which will consist of either Optimus Prime and Rodimus Prime or Megatron and Galvatron depending on whether you're playing as Decepticons or Autobots.
- Final Boss: The final boss fight is a Dual Boss, consisting of Optimus Prime and Rodimus Prime in Decepticon mode and Megatron and Galvatron in Autobot mode.
- Licensed Game: This is a video game tie-in to the 1980's The Transformers cartoon.
- Meaningless Villain Victory: The Decepticons' version of the story has the Decepticons defeat every Autobot in their way, but their victory in securing the Zel Quartz is ruined by Galvatron, Scourge and Cyclonus disappearing due to preventing their future from transpiring and the Zel Quartz being rendered powerless by Starscream taking it out into space without putting it inside his body first.
- My Future Self and Me:
- Both storylines involve Megatron working with Galvatron, his future self upgraded by Unicron in The Transformers: The Movie.
- One of the final boss fights in Autobot mode consists of fighting Full-Tilt, Soundwave and Soundwave's upgraded self Soundblaster from Transformers: The★Headmasters all at once.
- Nice Job Fixing It, Villain!:
- In one cutscene for the Decepticons, Megatron and Galvatron argue over which one of them is to blame for failing to find the Zel Quartz and nearly start a fight that will kill each other. While the other Decepticons panic, Starscream tries to egg both of them on so he can take leadership for himself, only to accidentally remind them both that they are technically the same person, and no matter who wins they would both be doomed. While all the other Decepticons think this was Starscream's true intension and praise him for his quick thinking, he silently curses to himself in anger.
- In both campaigns, Starscream steals the Zel Quartz for himself and takes it off the planet to install it in himself where he can't be interrupted. However, he doesn't know taking it off the planet renders it powerless, which means it is useless to everyone and fixes the Bad Future the future Transformers come from.
- The Stinger: After the end credits of either playthrough, we're shown what happened to Starscream after he made off with the Zel Quartz.