Nikita (TV series)/WMG

In the series finale, Alex is going to be the Big Bad.
"Echoes" has clearly shown that Alex has the potential for darkness. Nikita is aware of this potential and is trying to save her from herself. Nikita will fail.

One day, Alex will be Nikita's greatest enemy, and Nikita will have to kill her old student. Think Obi-Wan and Darth Vader but NOT IN SPACE!

Jaden will come over to Nikita's side
She probably thinks that Thom was Nikita's mole and Nikita left a recruitment tape in Division's network. Jaden might contact Nikita as soon as she's made an agent.
 * Except, in "Girl's Best Friend", she shows that she really is loyal to Division, as she not only completes the official mission, she also completes the side mission Percy was keeping secret from Michael.
 * And now completely Jossed by.

Jaden is working for someone else
And is gaining Percy's trust as part of that. Much of her behaviour around Percy is similar to how Alex used to act around him, as if she's working towards something.
 * Seems unlikely. But if that is the case, now we won't know until that person reveals himself/herself (see above theory).

Alex's mother is not dead
Alex only saw her father die. We haven't heard anything about her mother at all. It is very possible that her mother is still alive and might re-appear in the show (played by Peta Wilson).
 * Maybe she is the one who ordered Division to kill her family? After all, we don't know who made the order and Udinov's enemies is too vague. It's not Babylonian times. You don't become the CEO of a billion-dollar multi-national company because you killed the founder. You have to be someone in a legitimate position to step in. In other words, you need to be somebody who was not only known by Udinov, but pretty damn close to him. His second-in-command, maybe.... Or his wife.

Oversight will kill Percy
Given that he's blackmailing them with his black boxes. Once all of the black boxes are destroyed by Nikita they'll want him removed, along with agents loyal to him, the only named agent that is really likely to be loyal to Percy is Roan (Michael hates Percy, Birkhoff hates division (except the shiny tech, and being allowed to breath), Amanda could probably fool anyone assessing her (that and we have no idea about her past)). Furthermore it is likely oversight doesn't care about some of Divisions mercenary ops (as long as they don't interfere with oversights own goals) as it reduces the cost to them, however with another person in charge and not taking a (presumably) large portion of the commission fewer mercenary ops would be needed to cover Divisions costs.
 * But won't that cheat Nikita of the joy of killing him?
 * In a way, but Nikita isn't so much after Percy than trying to stop what Division does, Oversight killing Percy would allow the introduction of some of it's own members (perhaps specially trained assassins, who are trained from birth rather than from their teens, purely as a contingency plan). Additionally it could be used as further motivation for Nikita, as it would show the ruthlessness of Oversight. Furthermore she doesn't actually SEEM to be aware that they exist as a functional group rather it seems that she considers them to be some non-coordinated individuals in the government. Having an oversight assassin that has not really had any experiences outside of training and missions would be an interesting character if written well and could even be used as a 'dark side' version of Nathan, while simultaneously slowly developing ideas about morality. Besides Michael would enjoy killing Percy more due to his callous disregard for the recruits, perhaps someone from Oversight could manipulate him into killing Percy.
 * In "Pandora", the Oversight members we meet quite clearly don't like Percy and are only tolerating him because he's blackmailing him with the Black Boxes. At the end of the episode, which will probably be key to a move against Percy. And furthermore,   is revealed to be working for them, which means they would be more than capable of taking Percy down if and when the boxes are eliminated.

Alex's father was a super agent of Gogol and was training her to become an agent. Her family was taken out by Division in order to eliminate/weaken the competition.
Alex's flashback in "Free" supports this.

Alex's father was a renegade Gogol/Division agent attempting to take them down.
It fits with the "undercover agent falls in love with a civilian; Tragedy Ensues" recurring theme that the new series has going. And to make it to middle age, he must have been really good at hiding; at least as good as Nikita herself, if not better. He possibly even set things up so a renegade Division agent could take in Alex and train her (I'm a little fuzzy on the chronology at the moment so I forget if Alex's parents died three or more years ago).
 * Both this and the above were Jossed in "Betrayals" - Alex's father was killed just so that Division could install a more "Western friendly" person in control of his company.

Amanda will become The Starscream.
Out of all the named high ranking members of Division, she seems the most likely. Birkhoff is too scared of Percy to try anything (and really isn't in a position to take over Division anyway); what little we've seen of Roan suggests he's too loyal; and while Michael is opposed to Percy's methods, he's still loyal to the cause (plus, the whole "I Owe You My Life" thing). Amanda, meanwhile, seems like just the sort of Manipulative Bitch who would take advantage of Percy's weakening position (i.e. the destruction of his black boxes) for her own gain. Perhaps, when it comes down to the final box, she'll try and engineer an Enemy Mine situation with Nikita in order to take Percy down, while at the same time setting herself up to be chosen by Oversight as his replacement. We could then see which one of the three of them manages to Out Gambit the other two.
 * In "Pandora", . So I'd say this theory is panning out, even if the details aren't.
 * Confirmed in season 2.

Birkhoff will join Nikita's side.
He is a Boxed Crook who is only working for Division because he is being forced to, and before he was forced in, Shadow Walker was anti-government. Given half of a chance, he probably would like escape if he could.
 * The only problem would be a story reason: since in this show, information technology is the key to winning, taking away Division's tech guy would basically cripple them. I could imagine this happening in the series finale, though, to make Percy wish he didn't kill the Engineer for no reason.
 * Plus, when Nikita tried to use this logic on him in "Free", he turns her down.
 * Then again, in "Pandora",.
 * As of the second season premiere, he seems to have accidentally joined their side by . In the next episode

Percy is Nikita's father
Well, in the original series, Nikita's father did turn out to be The Man Behind the Man, and Percy does seem to have had an interest in Nikita back in the day...
 * In "343 Walnut Lane," it was revealed that, when Niki was just an ornery recruit, Percy had a plan where he would reveal her father as being a former CIA agent. The idea was to make her an enthusiastic agent. The other option, the standard one, would have simply been to cancel her. Ad we still don't know who her father is, since her supposed father was a fake and his name was purposefully left out of her dossier. If it didn't matter, they would just have said that he was dead, same as with the mother. So Nikita's father probably is or will be an important character. Why not Percy, same as before?

Roan will make it personal with Nikita.
Roan just got Harvey Twofaced by Nikita. He'd probably like a bit of personal revenge.

Nikita and Division will eventually have to unite to fight against Alex

 * Alex doesn't really seem to hold a very high opinion of Nikita or Division at the moment, if she were to become the head of Zetroph perhaps she'd have enough influence to destroy them all, leading to a rocky alliance between Division and Nikita.
 * In addition, as of the season finale, Alex seems to now be in alliance with, which would give both Division and Nikita further reason to bring her down.

Percy and Amanda had a romantic/sexual relationship
It's been alluded to in interviews with Melinda Clarke and Xander Berkeley. Plus, Amanda seemed to feel betrayed when Percy kept her out of the loop on Project Sparrow in a way that suggested that they used to be closer.
 * And when Percy broke it off Amanda turned against him and became The Starscream.
 * Confirmed as of the episode 'Sanctuary'.
 * Though she seems to have been The Starscream since long before then, if.

Max will end up in Nikita & Michael's custody

 * Currently, Cassandra is taking care of Max, but with the reveal that she's a deep cover asset for Gogol, and that Ari plans on activating her to assassinate Semak, it's doubtful whether she will survive the attempt - especially if she ends up on opposing sides with Michael and Nikita. Which means that once she bits the dust, Nikita and Michael have no choice but to bring Max with them.