Following from the events of the previous episode, Agent Fowler is sat down to explain recent events to his superior, the cynical and disbelieving General Bryce. Threatened with a military tribunal and Team Prime's termination, Fowler tries to convince the General that the Autobots are still on the military's side, but the General believes that Optimus Prime went rogue and has perished, failing to fully understand that Nemesis Prime was not the real Optimus.

Bulkhead acquires a top-secret formula, and the Decepticons come after him for it.

Jack tries to be impressive, with Bumblebee's help, but Knockout's arrivals sends things out of control.

The kids are stranded with Skyquake in an alternate dimension during a GroundBridge malfunction.

Starscream pursues other interests while Skyquake battles with Optimus Prime and Bumblebee.

Scraplets invade HQ while Optimus and Arcee patrol the Arctic, leaving Bumblee and Ratchet to repel the enemy.

Miko and Bulkhead go up against Starscream and Breakdown as they go to Greece to retrieve an Energon Harvester.

The Autobots try to claim a magnetic weapon before the Decepticons get to it.

Bulkhead is unknowingly shadowed by Miko as he goes to rescue Agent Fowler, who was kidnapped by the Decepticons.

The Autobots go on alert as the Decepticons return to Earth in the series opener, Meanwhile a group of humans find themselves with new caretakers after stumbling into the middle of the Autobot conflict with the Decepticons.

Bulkhead awaits a visit from his buddy Wheeljack, but his arrival does not go as planned.

The Autobots are attacked while helping Agent Fowler transport an implosion device.

Airachnid makes a deal with Silas to get revenge against Arcee and Jack.

The Autobots try to stave off an attack from Megatron's Terrorcons to protect their human wards.

MECH agents capture a Decepticon, and the Autobots mount a rescue.

The Autobots go in search of Cliffjumper, whose life signal is weak and find Megatron wielding the dangerous dark Energon.

Arcee must protect Jack when a routine mission is complicated by Airachnid's arrival.

Megatron controls Bumblebee from inside his mind and influences his behavior at HQ.

Two patrolling Autobots end up trapped in a cave with their enemies, Starscream and Megatron.

Bumblebee questions his worthiness to his team after he is compromised.

A Decepticon plague infects Optimus Prime, so Arcee and Bumblebee sneak onto the Nemesis to find the cure.

Wheeljack returns to Earth, hot on the the trail of Skyquake's brother Dreadwing.

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Megatron infuses The Nemesis w/ his own supply of Dark Energon which results in the ship taking on a life of its own with its own agenda. Meanwhile Optimus reluctantly decides to use the Spark Extractor in an attempt to bring the war to an end.

Megatron goes on a conquest to reveal the rest of the relics while Arcee and Bumblebee race him to New York City before Megatron gets there.