Optimus finds himself back on a deserted Cybertron, being chased by an army of mindless tanks. Locked in his original beastmode by a virus, and suffering from amnesia, his only option is to flee. One by one he encounters his old friends, and it becomes apparent that something is leading them... somewhere...
The Maximals split up and go in search of a new base when a mole-drone drone interrupts their much-needed training. But Blackarachnia drags Cheetor along to investigate the surface instead and discovers that Cybertron's archives have been erased. After having to fend off another drone attack, the four Maximals make their way towards the Council Chambers to find out who's running things.
The Maximals are attacked once more by Megatron's drones, while Rattrap is looking through Cybertron's backup files for a clue to what has happened to their homeworld. When they escape again, Megatron reconsiders his stance on sentient subordinates.
Optimus detects a familiar spark and sends the Maximals out to look it. Unfortunately all he finds is Tankorr, ready to ""smash beastbots"". Rattrap however, still stuck in beastmode, finds a ""transformation enhancer"" program - though it turns out to be a bit too much of a good thing.
Optimus discovers a Maximal bat hiding in the shadows. At first he flees, though when Jetstorm ambushes them he is forced to cooperate.
After botching a reconnaissance mission, and discovering his beastmode is weaponless, Rattrap's self-esteem hits an all-time low and he heads off to strike a deal with a weakened Megatron.
Optimus floods the underground levels with coolant while fleeing the Vehicons. Forced to go to the surface the Maximals end up in a graveyard with thousands of Maximals whose sparks have been removed. They are soon tracked down again, and in the ensuing firefight Black Arachnia and Thrust are trapped in a spark removal facility about to blow up.
While Optimus insists on meditating to explore deeper into the Oracle, Cheetor takes the rest of the Maximals out to probe Tankorr's mind to find out if he really is on their former comrades.
Rattrap and Cheetor face a dilemma in stopping the rampaging Tankorr without hurting Rhinox inside. Meanwhile Nightscream chases after Jetstorm to retrieve Black Arachnia's spark.
Megatron sends the diagnostic drone along with the Viecons to capture and study Nightscream in hopes of finding an effective way to purge his beastmode.
Optimus is now convinced that his mission is to return the organic life to Cybertron with the help of the green organic goo found in Cyberton's core. The first obstacle is however Rhinox/Tankorr, who decides to pay the Maximals a little visit equipped with the newly found key to Vector Sigma - capable of turning organic life into techno-matter.
While Rattrap discovers a growth acceleration program, Blackarachnia goes of to revive Silverbolt with some organic goo, and Megatron gets the key and sends Thrust and Jetstorm out to test it.
When he finds he no longer has control over the key equipped tank drones, Tankorr decides to provoke Megatron into action by showing Optimus the legendary ""plasma energy chamber"" in fake vision from the Oracle.
In the aftermath of the plasma/techno-matter storm, Optimus' spark floats free within the Oracle filled with guilt. Meanwhile the rest of the Maximals awake to find the entire planet off-line
Megatron's head floats unmoving in the air, but an automated defense system keeps the Maximals from accessing it. So Optimus tries to contact Megatron's spark while the others go in search for Thrust and Jestorm, hoping they can be persuaded to join.
The Maximals prepare to enter Megatron's fortress in search of the missing sparks. They decide on not bringing along Noble, but as the doors are about to close behind them he springs in and goes berserk, setting off the alarm.
Nightscream is attacked by the Viechons while out looking for any trace of Noble. When coming to his rescue, Optimus and Cheetor are captured by Megatron while Blackarachnia is busy luring Jetstorm into a trap she hopes will restore Silverbolt.
Megatron infects the Maximals with a virus that makes them unable to contain their frustrations, leaving them arguing continuously.
An unknown spaceship crashes down on Cybertron, and it's a race between the Maximals and Thrust to see who gets their first.
After the Maximals scrap Thrust and his drones for the umpteenth time, Megatron decides it's time to bring in some reinforcements.
Optimus receives a vision - a short glimpse at the locations of the captured sparks. He decides to split the Maximals into three teams, each searching for one of the places he saw.
While Megatron starts to devour the captured sparks to strengthen himself, the Maximals prepare an attack to free them.
Megatron is gone, but things are far from peaceful as old robot shells start attacking the Maximals.
The Maximals have control over the flying head, with the sparks safely inside. But Megatron is quick to order his replenished drone army to attack.
As Megatron awaits the completion of his new body, he orders his army to recapture the crashed ""head"".
The drones prepare the sparks for Megatron to absorb and Primal remains the only other transformer on-line to stop it.
