What if the Master is behind Miracle Day?
For those unfamiliar, the Master is an infamous villain from Doctor Who, the show that spawned Torchwood. He time travels using a machine called a TARDIS that's bigger on the inside than the outside.
I know Russell T. Davies has been insistent that Torchwood should never overlap with Doctor Who. But ever since it was revealed that PhiCorp's warehouse was bigger on the inside like a TARDIS, I can't shake my suspicion the Master is involved.
Miracle Day seems beyond the capability of PhiCorp. More likely, they're being exploited by someone more powerful for some purpose besides making money. Many, myself included, have wondered if the real motive is finding a way to kill Jack.
The Master has good reason to want Jack dead, particularly if the latter is the Face of Boe. In the Doctor Who episode "Utopia," the Doctor discovers a character is the Master in disguise thanks to a cryptic warning delivered by the Face of Boe.
I'm guessing the Master has realized that Jack is indeed the Face of Boe, and that killing him is the key to rewriting a timeline in which the Master suffers a series of humiliating defeats by the Doctor.