The opening scene shows Unicron, a space-roaming artificial planet,
grinding and consuming the peaceful robot planet Lithone, along with the
vast majority of its civilians. Only two ships escape, with Arblus and
Kranix as its only survivors, though both of them are later executed by
the Quintessons. A third ship almost escapes, but is sucked into Unicron.
Following the opening credits, the narrator states that the evil
Decepticons control the Transformers' homeworld, Cybertron.

The heroic Autobots are readying themselves on two of Cybertron's moons
for a strike against the Decepticons, preparing a supply shuttle for
launch to Autobot City on Earth. Their transmission is intercepted by the
Decepticons, who ambush the shuttle and kill its crew to use the ship to
infiltrate Autobot City on Earth without being detected. Meanwhile, on
Earth, Daniel Witwicky and Hot Rod race to greet the shuttle. They notice
its damaged exterior and spot Decepticons aboard the damaged shuttle, upon
which Hot Rod fires at the stowaways. After a brief battle pitting Hot Rod
and Kup against the Decepticons Blitzwing and Shrapnel, the Decepticons
begin their attack on Autobot City.

The outnumbered Autobots, including Autobot City Commander Ultra Magnus,
Blurr, Springer, Perceptor, and female Autobot Arcee, fare poorly. Ultra
Magnus sends orders to alert Blaster to radio for assistance from their
commander and leader Optimus Prime. An attempt to thwart the transmission
by Decepticon Soundwave fails, and the broadcast reaches Moon Base One where
Optimus is stationed. Optimus Prime and the Dinobots arrive to successfully
repel the Decepticon invaders, including the unstoppable Devastator.

Optimus faces Megatron in a battle that leaves Optimus mortally wounded and
Megatron severely damaged. The Decepticons retreat with Megatron and their
other war-wounded loaded aboard Astrotrain for transport back to Cybertron,
on the orders of Starscream. The Matrix glows in Hot Rod's hands before
being passed to Ultra Magnus. Inside Autobot City's walls, Perceptor alerts
the other Autobots that the wounds that Optimus Prime has suffered during
his battle with Megatron are fatal. The dying Optimus Prime calls on Ultra
Magnus to assume command of the Autobots and bestows him with the Autobot
Matrix of Leadership, which Optimus extracts from his chest. Optimus asserts
that the Matrix will light the Autobots darkest hour, right before he dies.

Back in space, Astrotrain's shortage of fuel prompts the Decepticons to eject
the dead weight of their injured including the protesting Megatron. This
leaves the remaining Decepticons to bicker among themselves for leadership.
Drifting aimlessly, the Decepticon castoffs encounter Unicron, who offers to
give Megatron and the others new bodies on the condition that they destroy
the Autobot Matrix, which, Unicron says, is the only thing that can stand in
his way. Megatron reluctantly agrees, and Unicron uses his power to kill
Megatron off, recreate, and reformat him as Galvatron, with his damaged
underlings fashioned anew into Cyclonus, Scourge, and the Sweeps. Unicron
provides them with a craft on which they travel to Cybertron, where Galvatron
confronts and obliterates the treacherous Starscream and takes command of the
Decepticons, as his alter-ego Megatron did before him.

Back on Earth, the Autobots are alerted as Unicron consumes Cybertron's two
moons, along with Autobots Jazz, Bumblebee, Cliffjumper and Daniel's father Spike
(who are ultimately rescued). Galvatron leads the Decepticons in another assault
on Autobot City. The Autobots board a pair of shuttles and flee toward their
threatened planet of Cybertron. Hot Rod, Kup and the Dinobots are shot down
over the planet Quintessa, while Ultra Magnus and company evade their pursuers
and set down on the planet of Junk for repairs.

Captured by Quintessa guardsmen, Hot Rod and Kup witness the sentencing and
execution of Arblus and are then subjected to a trial by Quintesson executioners.
Before the trial, they see Kranix, now Lithone's last survivor, who then tells
them about Unicron, before he's taken away by the Quintessa guardsmen to be fed
to the Sharkticons. At the trial, Hot Rod and Kup battle the Sharkticons with
difficulty, but luckily, they are rescued only by the arrival of the Dinobots.
Grimlock intimidates the Sharkticons to rebel against the Quintessons with ease,
while the Autobots escape. With help from the Dinobots' new ally, Wheelie, they
locate a ship and depart for the planet of Junk to join the other Autobots.

Meanwhile, Galvatron finds and hunts down the Autobots on Junk. Ultra Magnus
tries but fails to awaken the Matrix's powers, and then is obliterated to pieces
by the Sweeps. Galvatron steals the Matrix, stating that he intends to use it to
make Unicron his slave. The remaining Autobots are harassed by hostile Junkion
natives, led by Wreck-Gar, until Hot Rod's party touches down to befriend them.
The Junkion allies repair Ultra Magnus and volunteer a vessel to help the Autobots
fight against Unicron. Back in space, Galvatron attempts to subjugate Unicron
using the Matrix but is unable to unleash its power. Unicron, seeing that
Galvatron is underestimating him, transforms into a huge planet-sized robot and
attacks Cybertron. As protest against this, Galvatron opens fire on Unicron, but
Unicron simply swallows him up. Decepticon defenders scramble to counter Unicron's
attack, but he destroys each one of them, including Shockwave, Dirge, Thrust,
Ramjet, and countless others. As the Autobots reach the scene, Hot Rod crashes
his ship into through the giant's eye and finding themselves separated within
Unicron's body. At that time, Wreck-Gar and his Junkions fight back against
Unicron, but Unicron crushes their only ship, although they survived.

Inside, Hot Rod fights the recently consumed Galvatron. Hot Rod secures his grip
on the Matrix, and the power of The Matrix is unleashed, transforming him into
Rodimus Prime. Rodimus unleashes its power to destroy Unicron from within, but
not before he throws Galvatron deep into space. Rodimus leads the other Autobots
out of Unicron's body before it explodes, sprawling parts of the giant across
the galaxy. Reclaiming Cybertron, the victorious Autobots declare the beginning
of a new age of peace and happiness while the defeated Decepticons scramble away
to a burned world called Chaar. Ultra Magnus decided to step down his position
as leader of the Autobots, handing it over to Rodimus. The movie ends with
Unicron's monstrous head circling Cybertron, a dark replacement for the two moons
that once existed in days past.