This movie is related to The Langoliers
Only instead of passing through an aurora, only the people dying at that second were stuck in time. Zac wasn't the only one with doubts about the project
The reason that Perrin was the only body found in the lab wasn't because he was incinerated at Grid Control but because he evacuated the lab before bringing the Grid online. Assuming that Perrin was Zac's boss, he would've known about the incomplete programs or may have even overheard Zac using his dictaphone. So, he confronted the home office in a conference call, they gave him the runaround and he decided to clear the lab as a precaution. Humanity didn't disappear, just the people who died
Zac assumes that everyone disappeared as the result of "the effect" and they only survived because they died the moment the effect happened. But what if it's the other way around? No one actually died, the effect just created a new universe and anyone who died at the moment it was created ended up there. If so, the world they left is still very much around and the people there still alive. Depending on what happens, it's even possible that some of the people whose remains were found in the unstable universe survived in the stable one.The collapse of the Grid in the unstable universe may have resulted in Joanna and Api going back to the stable universe and reviving.
Zac develops the ability to hop universes
Being exposed to the effect at a possible epicenter may have changed his body in a way that allows him to trigger "jumps" between universes.