The Shadow Riders are one of many teams that resist the evil of the corporation Mys-Tech. They ally themselves with the mercenary Cable to rescue a tortured mutant named Matthew Ryan from the company. However, Ryan has secrets of his own that will come to threaten them.
As Cable approaches a covert MyS-Tech building he spots another man already on the premises. Cable is there for a suspected mutant that may be too powerful to allow MyS-Tech to keep him. Professor timeslides Cable in so he can get rid of the unknown man. The two engage gunfire and Cable subdues the man named Boot. Cable opens a time portal before inquiring as to Boot's purpose for being at MyS-Tech. Boot doesn't give and tackles Cable into the portal. Meanwhile, a mutant inside MyS-Tech let's out a shriek while being experimented on.
Since Boot hasn't checked in recently his teammate Roadie gets worried. She calls team leader Vorin to alert him. He brushes her off, as he's on the hunt for the next initiate. He senses death close and drives to a scene in which Death's Head II is about to kill a man. The man protests that Death's Head II has the wrong man - he's Rick Jones and not Mick Jones. This doesn't matter to Death's Head II and he moves in for the kill. The Hulk steps in at that moment and saves Rick. Vorin is disappointed that he won't get his dead body. He senses another person close to death and leaves Rick to watch Death's Head II and the Hulk duke it out.
In the future, Cable asks Professor why Boot was allowed through. It seems an interruption took place that negated any security parameters. Looking around, Boot seems to think that he died in this location. Cable has no idea what Boot is talking about and gets surprised when Boot flies passed him and back out the portal. Cable runs back after him to MyS-Tech's roof.
Back at MyS-Tech, the mutant is pushed far beyond his limits. He passes out. Workers inform Porlock, the techno-wizard in charge of this operation, state that the mutant's distortion is no longer affecting their scanners that two men are up on the roof. The security team that is sent finds Cable and Boot continuing their firefight from earlier. Boot turns his attention to the security team and lights one of the troops on fire. Vorin arrives as the man dies. He instructs Boot to bring the body to base. As the two men depart Professor informs Cable that the defenses are coming back up and he'd better get out of there. He timeslides out before getting stuck in MyS-Tech's energy shield.
At the Shadow Rider base, Boot informs everyone that the energy readings they were getting led him straight to a MyS-Tech base. He figures a giant bomb is being built there and mentions Cable thought a mutant was being held there. Regardless, Vorin doesn't want MyS-Tech having such a potentially dangerous weapon. He tells Boot to prepare the dead body to become the next Shadow Rider. The body is placed in a circle and Vorin fuses the man with images of past Shadow Riders. The man's body is reanimated with a bigger frame and some extra-normal powers.
A few hours later and Roadie picks up more energy readings from the no-longer covert MyS-Tech building. Boot recognizes that the defense systems will probably go down again and now would be the perfect time to attack. Vorin agrees and the team prepares for an assault on the building -- and the new guy, the former guard, will be with them.
Six months prior (events happen before Warheads #5): Mr. Grant and Rathcoole discuss a botched mission by the Malkuth Strike Troop in which only Che was a survivor. The men are skeptical about the report he gives of the Warheads landing in a very high tech and very well guarded fortress, resulting in the death of everyone else in the troop.
Three days prior, the Malkuth Strike Troop is in Egypt prepares to jump through a soon-to-open wormhole. Master Key is worried that the team isn't going to be ready since two are still putting their gear on. Boot chimes in that things could be a bit more fun if their preparations didn't prove good enough. He gets a slight reprimand from Che. The wormhole opens and the team moves through. Just then, Vorin appears and shoots the people monitoring the jump. He then awaits, knowing that only one of the Warheads will return.
On the other side of the wormhole, the Malkuth Strike Troop encounters a robot with uncanny defense systems. The robot calls for backup and the Warheads realize that they should just hold off the robots until the wormhole back home opens up. This plan proves fruitless when Cable appears and starts picking the team off one by one. The wormhole opens and Cable shoots Boot through it. Vorin is surprised that Boot appears and not Che. He figures Boot will do and preps the body for transport and transformation. He then leaves with Boot's body (to turn him into a Shadow Rider) while the Warheads structure explodes. Cable walks through the wormhole with a barely alive Che and wonders what is happening.