The story continues from Skynet's perspective of completing final tests of the first model 808 Terminator (a female called Aurora). It also shows Skynet initiating it's final solution to the human problem, with a co-ordinated mass nuclear carpet bombing of humanity with nuclear weapons strapped underneath Aerial Hunter Killers. As John and his group are formulating an attack on Skynet's mainframe at Thunder Mountain, his troops see the Aerial's and they decide that an immediate strike is needed and mobilize. There are two groups, one that will assault the mainframe and one that will attempt to knock out the facilities external power station.
The initial strike sparks off a volcanic eruption at a fault line bringing fiery winds along with the shock waves. These winds strike the Thunder Mountain facility just as John's group reach the outer doors. The ensuing chaos allows him and his commandos to get inside before the blast doors close. Once inside John's group have a running firefight to the main frame with John being lowered in front of it on a rope,just as the second group succeeds in causing an avalanche that flattens the power facility. John has a brief exchange with Skynet and fires his rifle into the mainframe screen and then falls from his rope and lands at the feet of a terminator who aims it's rifle at his head. The shot never comes as everything powers down. The final scenes show the resistance leaving Thunder Mountain into a sunrise, but then cuts to an image of John's powered down Terminator. The last panel showing red glowing eyes as it powers up back to life.
As with most comics based on film franchises, it may not be considered canon by future filmmakers. Notably, the alternate future of Terminator 3: Rise of the Machines established that the films' version of Skynet did not have a central mainframe, being more a part of the internet than a stand alone facility.