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Alex really was the one who bombed Grand Central Station
Everything has just been one big lie to pin it all on someone. When that person finally gets the blame and most likely killed, she'll have spun one hell of a Xanatos Gambit worthy of Kira.
  • Jossed. Elias framed her for it, but only 'cause he was threatened to do so.

Nimah's secret was supposed to be revealed during the opening assignment, but since the incident with Eric made it go undetected, they're keeping it up until someone outs them.
One of them literally says that Miranda told them to do something, so it's not like the administration doesn't know. And if they can keep this up at the FBI Training Academy, then they will be unbelievably useful in undercover work.
  • Semi-confirmed. It is sanctioned by Miranda, but only Miranda - she's trying an experiment to see if she can get the two of them to pass as one during training.
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Simon isn't actually gay.
He hasn't had sex with any of his four boyfriends, is visibly uncomfortable with another gay FBI agent hitting on him, and seems interested in Nimah beyond just his perceived interest in Arab/ Muslim culture. If you want to peg him as the terrorism suspect, it's possible he's faking his homosexuality to make him less obvious as a target.
  • The fact that his glasses were fake shows he was hiding at least something though whether or not this is part of that remains to be seen.
  • Possible case of Exact Words in episode 4, Simon tells Elias that he's not gay, "but my boyfriend is."
  • Confirmed in "Found".

Liam is behind the attack
The trainees learn a very valuable lesson in episode 2: a tip is only as good as its source. The audience will learn this lesson as well. Liam is the one who called in the tip about the attacker being a rookie agent, and we're expected to trust that simply because he's in a position of authority. The entire premise of the show is a ruse built by Liam to keep suspicion off of him.
Furthermore, it's implied that he already knew Alex's father personally before she showed up, which would give him insight into her and the ability to start her Frame-Up as soon as she gets into Quantico. What's likely is that Alex's father found out that Liam was mixed up in something less-than-savory. Unable to turn against his (friend? partner?), he resigns but says nothing. Liam is able to use the Parrish family agents as patsies in his own schemes.
  • Possibly confirming this is that tn the fourth episode we discover that Miranda suspects Liam, and Liam himself has been trying to push Alex out of the academy. A bombing of Grand Central could easily be blamed on a promising, but troubled, young agent wanting to follow her father's footsteps and, when she washed out, she took revenge. But since Alex stayed on, it ironically became even easier for Liam to frame her for the bombing.
  • And then Liam baldly claims that Alex "had something" on everyone at Quantico, which is so absurd as to defy belief.
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  • Confirmed as of "Right".

Simon isn't Simon
The Simon who went to live in the Gaza Strip was gay and wore glasses. The man who left four years later calling himself Simon is straight and doesn't need them. They call attention in America to the fact that, while it's possible to get into Gaza, getting out is a lot more difficult. That would explain why he's wearing fake glasses and pretending to be gay (the latter is a WMG in itself, but would explain his interest in Nimah, discomfort around Elias, the fact that he hasn't slept with his last four boyfriends, and his fake boyfriend in the pilot).
  • Jossed. He is who he says he is, but he lied about his circumstances: he was actually an IDF soldier, which gave him free range through the Gaza Strip on maneuvers and missions. He has since regretted things he did there and made up an alternate identity to try and escape his memories.

The Grand Central Bombing was a training exercise
Miranda really misses the old days.
  • Somewhat right. "Over" does suggest that the culprit/s are using the Grand Central bombing attack as a training exercise for the next big one.

Simon knows about Rainah and Nimah.
Considering how Simon lived in the Gaza strip, there's no **way** he'd be as ignorant as to think the side which Nimah tied the pin of her scarf could possibly have any extra meaning. He didn't ask that question out of curiosity, but to subtly let Rainah know that she and her sister's different ways of arranging their headscarves was a giveaway, even if Raina herself thinks he did it unintentionally. Simon's actions have constantly been reinforcing the twins cover, both by continuing his friendship despite personality differences (the way Simon kept hanging out with Rainah even after Nimah was incredibly harsh with him), as well as how he subtly points out cracks in their cover with 'unintentionally observant' comments (his comment to Rainah that she shouldn't feel exhaused when they've been doing this routine 24 hours for the past month). The comments especially are both too observant and helpful to be anything other than deliberate warnings, deliberate hints for the twins to fix cracks in their facade. Why Simon doesn't let on that he knows and chooses to subtly help out is, however, a mystery.
  • Jossed. He just walked in on them in "Go" and was clearly upset that Shaw did it.

Everyone or at least most of the students got something to do with the bombings...and they're all pinning it on Alex.

Caleb was involved with the bomb and Miranda's son, and his father is covering for him.
Caleb's father says that he's a danger to himself and those around him, and had to stop him himself when he risked other people's safety. It's possible that Caleb is part of the group that convinced Miranda's son to plan his shooting. However, Caleb is too wrapped up in his own psychological issues to realize the consequences or that he did anything wrong, and his father has too much pride to admit that his son has violent tendencies and could cause serious damage as an FBI agent. This forces Director Haas to walk the line between protecting the world from his son and protecting his own reputation. Director Haas is also the person framing Alex, as he likely has access to all the info Liam does and decided that should Caleb do something bad, like set off a bomb, Alex would be the perfect patsy. He's also one of the few people with the authority to remove Miranda from her position as Quantico director, which he may have done because she was getting to close to figuring out the connection between Caleb and her son.
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  • Jossed. Elias was in on it, but only 'cause he was threatened to do so.

The doctor who falsified evidence is the one who planned the bombing.
She notes that she knows how to stay in a security camera's blind spots, and she's more than just a bit obsessed with murder, both on the individual and mass scale.
  • Debunked. She framed an actual serial killer with another murder case she worked on with some FBI agents.

Shelby is still being conned.
How convenient of Khaled, the "husband" of Haifaa, to show up and claim she was kidnapped after Caleb basically blew the whistle on her. Now he can ask for more money to pay the phantom "kidnappers", then scoot back to Saudi Arabia with one last payoff.
  • Confirmed.

The Sistemics are the ones responsible for the Grand Central Bombings

Shelby's parents arranged the bombings
  • Her parents originally hid to escape being tagged with responsibility for aiding and abetting the 9/11 attacks through Al Qaeda's use of their software to aid in logistics planning. They claim to not have known about this illegitimate usage of their software, so being tarred with that brush would indeed have been unfair. However there is no reason to ever believe they were being truthful; ergo, if they stood to gain financially from the Grand Central attack (as they did from 9/11 indirectly, by getting Shelby to funnel money to them without her knowledge), then getting Shelby to go along with it on the promise of being able to reconnect with them might have been fairly easy.
    • Averted. They gave their tech to a contact in South Asia, which was later used by Al-Qaeda. They only ran 'cause they're concerned about being arrested as accessories to the 9/11 attacks.

Senator Haas is behind the bombings.
  • It's all part of a grand scheme to get herself elected on her security and defense platform, and Caleb may or may not be in on it.
  • Hinted at being confirmed as of the finale.

The episode titles give clues as to who is involved in the conspiracy in Season 2.
  • For example, KUDOVE refers to the CIA Deputy Director of Operations.
  • "Lipstick" appears to refer to Miranda's lip gloss.
  • STESCALADE is cryptonym, like KUDOVE, and refers to bugging operations by the CIA in the 1960s. Given that the bug Ryan and Alex planted was interfered with by another and other revelations regarding Miranda's doings, she could have tipped off the rogue group to do their own bugging operations.
  • KUBARK is another cryptonym that refers to counterintelligence operations. Given that Owen seemed to be asking questions of people in the CIA counterintelligence division it may be he was actually probing for who could be recruited into the rogue group.
  • KMFORGET is a cryptonym that refers to CIA media operations in which they would plant a story in foreign media, hoping to have it reprinted domestically within the USA to raise that story's profile for propaganda purposes. This could refer to which branch of the CIA is involved in the rogue group. Given that Owen had a double purpose in running his CIA recruits on an intelligence op, framing the reporter who exposed him with Leon's help suggests that Leon is in the rogue group.
  • "Aquiline" refers to an eagle-like facial characteristic, so it is likely a code name.
  • LCFLUTTER is a cryptonym that refers to using truth drugs in interrogation. In the actual episode, the AIC breaks Alex by torturing Dayana and threatening to kill her with a hammerblow to the base of the skull. This reveals that someone in the group knows the methods taught to Alex on the Farm.
  • ODENVY is a cryptonym that refers to the Federal Bureau of Investigation. Someone from the FBI almost certainly is aiding the rogue group, so it is likely to be revealed who exactly is involved. It's Ryan.
  • CLEOPATRA refers to the use of seduction techniques. Owen has the recruits use them in a wedding situation.
  • JMPALM refers to "removing" major political figureheads in Latin America, and agents involved in said operations. Owen runs an operation against the Venezuelan embassy.
  • ZRTORCH refers to communications between CIA officers and defectors. Owen employed methods of communicating with a German asset he once had.
  • FALLENORACLE is a CIA cryptonym for a secret National Security Agency (NSA) catalog database. Owen runs an op against the NSA to challenge the recruits to remove all information about themselves. The AIC uses it as a mission within a mission to tap into the NSA's feeds.
  • EPICSHELTER is or was a secret operation conducted by the National Security Agency (NSA), in which malware employed against other governments' computers could compromise them if necessary. In a sort of analogous move, Lydia uses the contents of the hard drives stolen at the G20 in order to compromise the USA by revealing all its intelligence accumulated over several decades.
  • After the mid-season finale, the focus changes to looking beyond the AIC to a greater conspiracy. LNWILT is a CIA cryptonym for the United States Counter Intelligence Corps, and obviously refers to the formation of the secret group composed of Alex and five other people, in order to track down said conspiracy's leaders.
  • MOCKINGBIRD refers to the CIA's recruitment of American journalists. In the episode it is revealed that the conspiracy manipulates news media in order to hide their pursuit of those who would otherwise reveal names and other information.
  • MKTOPAZ refers to the CIA's technical services division. In the episode much of the action revolves around the use of exploiting computer weaknesses to get information, as well as the use of mobile surveillance.
  • ODYOKE refers to the US government itself. The team has to try and get a bill stopped, and they realize one of the collaborators in the conspiracy could be in line for the Presidential succession.
  • KUMONK refers to the Office of Political Analysis. The team has to analyze potential flashpoints and determine why the collaborators would pick one particular one to inflame. As it turns out, in ths episode all the overarching collaborators influencing the AIC and other groups are revealed.

Lydia is in the rogue group
  • As revealed, she was badly hurt by her father calling in favors at the CIA to get her reassigned to a teaching position, so it stands to reason that she would lash out by joining the rogue faction (in addition to the cabal's ideology of expanded surveillance powers being potentially appealing to an agent used to working on her own in foreign countries).
  • Confirmed.

The biotech company boss will become a Big Bad
  • In season 3 episode 2, "Fear and Flesh", Warren Renway, the CEO of a biotechnology company, is found to have covert links with right-wing, white-supremacist organizations. It's not clear if he was arrested as part of the FBI bust, so if he's still freely moving about he may end up being connected to further Villain of the Week episodes.

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    Major Spoilers 
Miranda was recruited unwillingly
  • The rogue group is holding her son hostage and in doing so has forced her to play along or he will die.
  • Jossed.

Miranda has a team undercover inside the building
  • The more that's revealed, the less likely it seems that Miranda is entirely on the side of the terrorists with no other plans. What are the chances that she, Will, and Nimah are all working with the terrorists?
  • Confirmed. Miranda joined the anti-AIC Citizens Liberation Front to keep the FBI out of their way while they exposed the AIC.

Raina and Nimah have switched multiple times
  • The two of them are working together again to pass along information to the FBI by being within both the group of hostages and the terrorists. This would explain why Raina passed along the boiler room comment to Miranda, because if Nimah had really been the one in the room the whole time and working with terrorists, she'd have no interest in conveying that information.
  • Appears to be Jossed.

Nimah, Raina and Miranda created the AIC
  • They wanted a way to entrap would-be lawbreakers within the CIA. What better way than to plant the idea of the very organization Alex and Ryan are chasing after? Through their moles in the "AIC" they can easily run covert operations like stealing all the world's intelligence data while the world is distracted by a terrorist attack.
  • Jossed. The actual leader is Lydia Hall.
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