The 25th episode of Transformers: Prime continues from the last episode with
Optimus Prime single handedly taking on the rock manifestations of Unicron.  Optimus tells the other Autobots to stay at their based as the fight is his and his alone since Unicron is after a Prime.  Optimus is subdued under a joint attack of Unicron manifestations as the title sequences roll.

Unicron is about to finish off Optimus Prime when the other Autobot's arrive on the scene having disregarded his orders.  They explain to Prime that if Unicron is after him, it's even more important that he survives.  Prime eventually agrees and the Autobot's start to fall back fighting off more of Unicron's manifestations as they go.

As they head out into the desert Unicron manifests himself from an entire mountain, dwarfing the Autobots.  He is about to crush Optimus under his foot when the Autobot's are saved by an unlikely source ... Megatron.  The Decepticon destroyed the rock behemoth by blasting him through the back of the head and out of his right eye.

Megatron requests a truce with the Autobot's against their common foe. His logic is that only a Prime can defeat Unicron but only he can hear Unicron's thought as he is connected to the chaos bringer through the Dark Energon that is infused within him.  The Autobot's are unsure and do not trust the Decepticon, who tells them to return to their HQ to think about it whilst he keeps Unicron busy.  The Autobots do indeed do this and return back to their base to discuss the potentially alliance whilst Megatron takes on more of Unicron's spawn.

The Autobots discuss the pro's and con's of the alliance and eventually decide that it is their only course of action.  They will work with Megatron and use the Matrix of Leadership to defeat Unicron who is the Earth's core.  The Autobot's open up the ground-bridge and bring Megatron into their base as he has the co-ordinates of Unicron's spark chamber which is where they plan to head in order to defeat him. Before the group leave, Prime gives Jack the key to the ground bridge trusting him with it over Ratchet.

Whilst this is going on the Decepticon battle cruiser is shown in orbit where Airachnid says that the Decepticons must prepare for life without Megatron as their leader as, to her, it appears they he has left them and gone off alone or fled.

Back down on Earth Megatron, Optimus Prime, Arcee, Bumblebee and Bulkhead all travel through the ground bridge into the heart of Unicron, or into "The Heart Of Darkness" as Megatron referred to it, leaving the Humans and Ratchet behind.

The episode ends with the unlikely group making traversing the bridgeways with what appears to be Unicron's optic falling them.