Just throwing in my two cents here, I think they're going to retcon Gat's death in IV like this:
1.) Gat didn't actually get killed in the plane debacle (as we only heard the radio systems get shot out). The Zynyak abducts the plane with Johnny in it (remember, you never actually find either the plane or Gat's body in The Third, and there were hints suggesting there was never actually a crash to begin with through out the game). Loren was just spurting smoke out his ass about killing Gat to try to intimidate you (he's the Saints Row version of Doctor Evil, of course intimidation through bullshit is in his nature). You shooting through the front of the plane and crashing through it without seeing Gat? He could've been fighting off some of the MorningStar goons in another compartment of the plane, they were able break into the cockpit after all. Zombie Gat? Either, a.) Another clone from Loren to show "proof" of killing Johnny, and someone with voodoo power, likely someone from Eye for an Eye, resurrected the clone's body. (For those wanting to dispute this with The Trouble with Clones campaign, remember Loren probably hired a group of top genetics to create clones of Oleg, the procedure itself, and probably got some of the world's best equipment and computing technology money could buy to do so. At best Jimmy probably could imitate the technology and procedure using much cheaper alternatives, and probably based the cloning technique from how it was done with Oleg, but doesn't have Loren's resources, thus accidentally creating the brute "Tag".) Or b.) Loren probably had one of his goons go to Image as Designed to look like Gat and then killed him, again for "proof", as we already know the miracles those plastic surgeons can perform.
2.) If Johnny WAS originally killed at the beginning of The Third, and Johnny in IV is indeed a clone, either it could be a.) Jimmy, Kinzie or one of the other intelligent Saints (or, Saints fans) might've used some Zynyak cloning tech to clone Johnny. Think about it, how the fuck do they have so many soldiers that look so alike? Just switch out the master sample with one from Gat, and voila! The killing machine is back. Or b.) As this is a good point:
im thinking gat is a perfect clone but not of alien origin.
The Saints could just build upon the tech Loren used, and use that to try to bring Johnny back as a government initiative after the Protagonist gets elected, or at least something along those lines.
Just a couple of theories.