SIEGE begins in the final hours of the devastating civil war between the Autobots and Decepticons. The war that has torn apart their home planet of Cybertron is at a tipping point. Two leaders, Optimus Prime and Megatron, both want to save their world and unify their people, but only on their own terms. In an attempt to end the conflict, Megatron is forced to consider using the Allspark, the source of all life and power on Cybertron, to "reformat" the Autobots, thus "unifying" Cybertron. Outnumbered, outgunned, and under SIEGE, the battle-weary Autobots orchestrate a desperate series of counterstrikes on a mission that, if everything somehow goes right, will end with an unthinkable choice: kill their planet in order to save it.

With the Allspark gone, Megatron is forced to confront the harsh reality that his Decepticons are trapped on a dying Cybertron. Meanwhile, lost in the darkest reaches of space, Optimus Prime and his team embark on a desperate mission, unexpectedly running into ... the spacefaring Mercenaries.

The frantic race to locate the Allspark first culminates on a strange planet as the future comes crashing through to the present day.