The below storyboards can be seen in full at the Sunbow and Marvel Productions Script/Storyboard Archive. They contain numerous differences to what's seen in the movie, including several scenes and sequences that were cut, dialogue differences, and some scenes that would later be edited so they are shown earlier or later.

The big question many fans have is if any of these cut sequences were ever animated. As of 2021, only one piece of deleted footage has been found, showing an Autobot running towards the fallen Optimus Prime (see the sequence 8 page for more details).

Sequence 1:
Unicron attacks Lithone.

Sequence 3:
The Autobots launch their shuttle.

Sequence 5:
The Decepticons attack the Autobot shuttle.

Sequence 7:
The Autobot City battle begins.

Sequence 9:
The death of Optimus Prime.

Sequence 11:
The Decepticons fight over who should be leader.

Sequence 13:
Starscream's coronation.

Sequence 15:
The Autobots launch the shuttles.

Sequence 17:
Hot Rod saves Kup from the squid.

Sequence 19:
Kup and Hot Rod encounter the Quintessons.

Sequence 21:
The Dinobots encounter Wheelie.

Sequence 23:
The Autobots repair their shuttle.

Sequence 25:
Galvatron confronts Ultra Magnus.

Sequence 27:
Unicron attacks Cybertron.

Sequence 29:
The Dinobots attack Unicron.

Sequence 2:
The opening credits.

Sequence 4:
The Decepticons learn of the Autobot's plans.

Sequence 6:
Hot Rod and Daniel are attacked by the Decepticons.

Sequence 8:
The rest of the Autobot City battle.

Sequence 10:
Unicron learns that the Matrix has been passed on.

Sequence 12:
Galvatron, Scourge and Cyclonus are created.

Sequence 14:
Unicron destroys Moonbase 1.

Sequence 16:
The Decepticons attack the Autobots in space.

Sequence 18:
The Autobots crash land on the Planet of Junk.

Sequence 20:
Unicron tells Galvatron to go to the Planet of Junk.

Sequence 22:
Unicron attacks Moonbase 2.

Sequence 24:
Hot Rod and Kup are put on trial.

Sequence 26:
The Autobots encounter the Junkions.

Sequence 28:
Hot Rod finds Galvatron.

Sequence 30:
Daniel saves Spike.

Sequence 31:
Hot Rod fights Galvatron.