Starting shortly after the events of Oblivion, Margaret's team which had just been bolstered by new recruits find themselves besieged by Ray who declares war against them through a holo-message while presenting himself in person during a galactic meeting revolving around Neo-Hydra territory. Ghost Rider, a long time veteran, is the first to be consumed by Ray's power as he finds himself erased completely from the present timeline.
Shortly afterwards, Ray has an army of Immortals supported by Ray clones who pilot HMVs composed of nano-machines assault Automation in an attempt to stop Margaret's team from using the time machine to stop him. Their appearance is made possible thanks to Ray taking control of the facility that would end up producing the clones of Wraith, asserting control of the Immortal race in his new timeline, and his access to Masquerade's time machine allowing him to transport his army to any place in the timeline to enforce his will.
The team barely manages to escape through the prototype time machine constructed by the brightest of Automation, but they end up losing Lyra who sacrifices herself to buy time. Eventually the team find themselves transported to 91AF. Without any way to progress due to the need for a Forefather's blood or power being the main source of power, the team is forced to search for Axel's old team on Vegas, assuming that they might know the whereabouts of the remaining Forefathers.
The team splits off, each carrying out their own task, however, conflict arises when members of Axel's team are stirred into conflict with Margaret's by a clone disguised as Axel. When both sides try to resolve the conflict, the disguised clone detonates a bomb strapped to himself. Meanwhile, Axel finds himself beset by Ray clones with Dreamweaver soon appearing. After Dreamweaver's attack, it is discovered that Thor, the sole surviving Forefather from the climatic battle on Homeworld had been captured by Axel to be sold as a prisoner to the Neo-Hydras. Thor escapes after being released while both Axel and Margaret's team find themselves forced to tactically retreat in the direction of the ruined city of Gonair, the former home of the Jackals.
The fighting ends up with the majority of both teams making it to the rendezvous point, but Lucas is captured. While the Margaret and Axel's team recuperates with much explanation between the two, a Ray clone manages to convince Lucas to betray the team and give away their position. Achillies, who led an Achean assault against Margaret's team is later executed for letting members of Margaret's team escape due to his codes of honour.
A massive force is sent to snuff out the combined teams of Axel and Margaret. While the fighting initially goes well, Ray's force is simply too great and eventually Margaret's team is defeated and captured, but this is not before Guildstern manages to escape in the time machine, using the recently deceased Achilles as a means to power the machine.
With the team captured, Ray has Margaret's team imprisoned on what he calls Utopia with their minds altered to have no memory of their past lives before being placed into new bodies. Living false lives, the team goes about unaware of what truly goes on outside the domed city they were placed on. Unknown to them or Ray, however, are members of a resistance that still thrive despite Ray's attempt to quash all resistance using his control of time and his infinite army.
At one of the major gatherings on Utopia, the resistance makes it move and despite some resistance, manages to retrieve the majority of Margaret's team and have them transported back to the main timeline. The retrieval is costly and only one member of the rescue team manages to survive who happens to be a cybernetically enhanced Sprocket.
With the old team having returned to their old bodies, Margaret, uses her unique abilities thanks to her hybrid status of human and HMV which has been furthered by limited psychic modification sends a message down the various timelines using the Monitor's network. It is from this that she also learns that the original Ray had linked himself with the Monitor to put himself to near god-like status. Upon learning of this, the team prepares to assault Automation once again to return the galaxy to the way it was.
As battles erupt all across the galaxy and various timelines against Ray, Margaret's team dives onto Automation and fights their way to the Monitor's core. The clock is ticking, however. The gargantuan form of the Monitor's body previously seen by the team during their first battle on Automation arises and begins to tear into their supporting assets in space.
Slowly, the team manages to pick away at Ray's HMV avatar defending the core, but Margaret has only a spark left in her after she transforms back into her human form as a sort of sacrifice to defeat Ray's avatar who took control of her HMV form as he lay on the brink of defeat. Before anyone has a chance to argue or stop him, Mack removes Ray from the Monitor's systems and links Margaret in his place to save her, despite any objection her mind might of had.
With a new overseer controlling the Monitor the galaxy slowly return back to normal and the team returns back to their time line to carry on with their lives be it better or for worse.