So far, the series is all about setting up games and missions for the trainees, right? So, what if the bombing is all just one big game, too? A game that, like the trainee missions, was set up by the FBI.
My guess is that the show is setting up this bombing as a ploy, both for the public and as Alex's final mission before she graduates, because I think the FBI has something special in store for her — an elite covert mission that will require her to give up her life and go undercover.
The world will think she's a terrorist behind bars, but by Season 2, I'll bet Alex is working closely with either the FBI or the CIA as some sort of secret agent.
The show supports this theory in multiple ways.
First of all, they're having Alex closely watched and even followed before she's ever accused of the bombing.
Multiple times throughout the show, characters suggest that you have to be willing to give up your life for the sake of the FBI, such as Booth's quote on the last episode when he said, "If you're not willing to sacrifice yourself for your country, why are you here?"
Also, why is it that every member of Alex's trainee operation seems to now be involved in some way or another with the bombing? More likely, they're all involved in this scheme somehow and are setting Alex up, whether they realize it or not.
As Miranda said in this week's episode, "Survival and sacrifice: They go hand in hand. Out in the field, you have to stand with your fellow agents, no matter the cost. This job will test you. It will push you beyond the limits. It will throw curves at you and it will never not surprise you."
Natalie perfectly displayed this on this week's episode, when she let Alex and Booth go after she caught them in the alley. Why would she just let them go? She's the one who set up the raid. She's the one who has been pursuing them without any leeway. And she has them and just lets them go? She's choosing her team over the FBI, just like the game wants her to.
I also have a theory that Alex's dad is still alive. Not just alive, but was taken into the same covert operation that I think the FBI is grooming Alex for. I think she probably did, indeed, shoot him as a child. Or, at least, she thought she did. But we don't know any of the circumstances surrounding what happened after he was shot or what happened to his body or how the FBI handled the death of one of their own.
Either that or he really is dead but was part of this covert operation when he died, which is why the FBI is now watching Alex — to see if she will be a suitable replacement for him on the team.
My guess is that we'll see Alex arrested near the end of Season 1, only to be told that the bombing was never actually from an underground terrorist but from the FBI themselves as a controlled test.
By Season 2, she'll be hunting down the United States' biggest terrorists. And she'll be able to get close because all of them, and the rest of the world, will think she's an escaped terrorist herself.
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