The comic book:
The Zombie Apocalypse WAS bird flu.The government just didn't tell the people the whole story of what happened when you were infected.
If the comic is continued, current members of The Protomen will appear.To keep up with the times.
The comic is a dramatization of a Tabletop RPG game.Much of the craziness that happened was due to fumbled die rolls.
The TV show:
Holyoke is actually a Well-Intentioned Extremist
- Consider the events of "How To Stay Alive In The Woods" and "The Dharma Bums": Holyoke has been spending both episodes trying to get Amy killed, and during the seance, he calls her a "doorway" and tries to force her to slit her throat. Combined with creators mentioning (in the "Behind The Scenes" featurette for "The Dharma Bums") that the murders are ritual sacrifices to summon the demon depicted on the map Sykes found in the Pilot. If you take Holyoke's comment to mean that the demon will use Amy to enter the world, then his attempts to kill her can be interpreted as a desperate effort to stop it.
- Confirmed in "The Devil Inside". Not only that, but Amy was the real villain the entire time.