The first issue depicts the Battle of Tyger Pax, and how Bumblebee and Arcee's contingent of Autobot troops hold the line against Megatron's attacking Decepticon army as Optimus Prime prepares to blindly jettison the Allspark into space. In the end, Bumblebee succeeds in detaining Megatron, at the expense of his own voicebox being ripped out.
The second issue illustrates Megatron's exhausting search for the Allspark and how the journey leaves him vulnerable enough that as he finds the Allspark on Earth, he is too weak to avoid being frozen in the Artic. He is discovered by a sailor named Witwicky, and eventually falls into the hands of a covert branch of the US government.
The third issues shows how Sector Seven, a highly classified branch of the US military, has been hiding and studying the 'Mega Man' since its discovery in the Arctic, and how they witness the arrival of a similar being, who upon arrival on Earth, disguised itself as a yellow Camaro.
The fourth and final issue possibly wraps into the movie as the Decepticons, led by Starscream, land on Earth and encounter the military for the first time. However, the issue also shows how Sam Witwicky is given an antique pair of eyeglasses passed down from a seafaring ancestor of his back in 2003. He doesn't find them all that special, and decides he might be able to sell them one day...and with the money buy a car...