Well I've stated my theory already. It even made it onto the latest episode of We're Not Dead before being torn apart by Ra1th and nikvoodoo. But I'm sticking with it to the bitter end.
With all the build up with the helicopters, I seriously doubt the season is going to end without them getting off the ground for the trip to Fort Irwin. So I'm predicting the Tower folks get into some kind of trouble (surrounded by Mallers, zombies, etc..) and have to make a mad dash for the helicopters. Things get tense but ultimately they make it off the ground and to Fort Irwin and the season ends with them landing and finding that someone is already there. Probably someone with knowledge of the outbreak.
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