There are different sets of clones out there besides Sarah and her group.It's possible that whoever made these 'Orphan Black' clones would have at least one other set to compare sample sizes.
Blond Evil Clone
Sarah is the only one of the clones who can have children.Alison seemed very surprised to hear that she has a biological daughter. And Helena did seem to sense something special about her.
Sarah is the original.
Beth's suicide wasn't a suicideShe discovered something important about the clones and was drugged or Brain Washed into killing herself in order to shut her up. It would explain a lot, like the unusual timing of her decision to throw herself in front of a train. (If you were trying to protect a bunch of clones of yourself from a crazy murderer, would you just kill yourself and leave them to deal with the fallout?)
Alison will eventually dieShe's hot-headed, isn't good at hiding how she feels (sure, Alison, repeatedly confront and physically assault the guy who's possibly in on your clone conspiracy and monitoring you like Paul monitored Beth; nothing will happen), and while she makes a big show of being able to take care of herself for the sake of her children, she doesn't seem to be too good at following up with it (her hesitance to shoot Felix when she first met him).
The clones are not entirely identical.When having dinner with Dr. Leekie, Cosima mentioned a transgenic cloning patent. What if each clone was given a different genetic modification as a test to see which would produce superior results? Using clones to test biological outcomes is standard practice in lab experiments. The original would be the control.
Kira will turn out to be the ultimate goal of the cloning experiment.Kira does seem to be very bright and perceptive. What if the goal of the cloning experiment was to introduce "superior" genes into the germ line with the goal of breeding a more advanced version of humanity? As the only biological child of a clone seen so far, Kira would be very interesting to the Neolutionists.
There's something wrong with Helena (aside from the obvious mental issues).In nearly every scene she's been in, she's shown eating something. Sarah even lampshades it by asking if anyone feeds her "where [she] come[s] from". It's usually something high in sugar - apples, muffins, jello which she even added sugar to, ice cream, and what looks like either packets of sugar or Pixi Stix. She possibly has some sort of undiagnosed major health issue which is causing this massive need for eating which could cause severe problems in the future.
Allison and Cosima are going to develop health problems.Katja had an as-of-yet undetermined health problem, and, noted above, Helena might as well. It could be related to a breakdown of their DNA, and if so, something may start cropping up in Allison, Cosima, and/or Sarah. Allison's already been seen in at least two scenes popping pills, though they could have just been for a headache given the context of said scenes. Either way, this could also help pinpoint whoever the original is.
Leekie's secret ally is the original.The woman with the bob haircut shown with her back to the camera, who tells Leekie that blood is thicker than he thinks. From her voice and the vague reflection in the window, she could be another Tatiana Maslany character.
Helena's not dead.She has the same Healing Factor that got Kira through the car accident. This would also explain the massive food intake referenced above, as she was healing from the rebar injury at the time. Besides, she's just too great a character.
Mrs. S. is the original.She does somewhat resemble Sarah and the others and she is highly protective of Sarah and Kira. And it looks like she might have been involved with some secret project back in the day. She might have been at least a donor of genetic material and that might be why Sarah was brought to her in the first place.
Being raised by Mrs. S. is the reason Sarah had a kid and none of the others could.If Mrs. S. was involved with a/the cloning project she might have known how to treat any health issues Sarah had as a clone.
Felix had been abused physically before being fostered by Mrs. S.Whenever Felix is manhandled and Sarah is around, she is incredibly quick to stop it. When the lady in the bar flicked a towel at him, he commented that he had a "traumatic childhood". I dunno, I think that Sarah tries to shut down all the negative contact on Felix in case he has a flashback, or a panic attack or something along those lines. Felix obviously knows his triggers, and so he tries to avoid them too - such as an object whipping at him (like the towel).
Kira escapedSarah had Kira put together an emergency bag, that not even Mrs. S knew about. When the house was attacked, Kira grabbed the bag and ran. That's why her window was open at the end.
There are parallels to the clones:Cosima - Katja ... Allison - Helena - Beth ... Sarah - Rachel ... As we saw from the finale, Cosima is sick, much like Katja was. And if you think about it, Allison is going down a slightly abnormal path, from a psychological standpoint, much like Helena. Additionally, from what we hear about her, Beth was withdrawing emotionally, and she committed suicide. Sarah and Rachel are both savvy people, even though they are on opposite sides of the fight. They are both seemingly in charge of the situation, slightly like a batman gambiter. Allison and Helena's parallels are frightening when you think about the fact that Helena was pushed towards insanity by the many many years of abuse, while Allison is living a supposedly perfect life, yet she is finding herself increasingly paranoid and violent.
Felix is in on the whole thingFace it, he's too likeable and has too many fans not to turn out to be a traitor later on.
The clones are the result of a global conspiracy and/or alien technologyPer a forum post on the Orphan Black Wiki:
It's hard to believe they succeeded to clone humans in 1984 because the original Mac was just being sold along with the Commodore 64 and the Cray Super computers (cost $33 million) were as fast as a 1995 Dell Dimension. It would take 1 MILLION of those Cray II's to calculate a fold in a chromosome strand in a day at a cost of $33 TRILLION. The human Genome Project was just starting in 1984 and wouldn't be completed for decades (and still has a few uncharted regions).
This is a sci-fi show and for them to have cloned humans in 1984 I'm thinking they had alien help. Maybe a global conspiracy that would need the resources of the USA, Soviets, Germany, Japan, and other countries with vast hidden sections in their budgets to pull it off.
Alison will eventually suffer a Sanity SlippageShe will discover that Aynsley wasn't her monitor and adding that on with her drinking and pill-taking plus the fact she let Anysley die will soon make her lose her mind.
There will a prequel episode that expands on Beth's life leading up to the suicideAs well as expand on her (and to an extent, Katja's, since she died shortly after Beth) relationship with Alison and Cosima in looking into their cloning.
Beth isn't deadTake a look at the body shown in the morgue, the scar Beth has on her neck isn't there. Considering the scar plays a big part in Paul figuring out Sarah wasn't Beth, it was odd for it not to have been there. Granted, it might've slipped the minds of the creators but it would have made for some Foreshadowing. Also, as mentioned above, Beth's suicide is a little too weird. Beth is a cop. A cop who was on medication. She kills herself by jumping in front of a train. She could have merely shot herself, or overdosed but she chose a train. Perhaps the clone who jumped in front of the train was a clone Beth convinced to impersonate as her while she went on the down-low. Maybe the clone killed themselves because they couldn't deal with it. Either way, it's more of a long-shot but her death just doesn't completely add up.
Kira is going to receive an artificial growth boostWith a year between seasons, the little girl playing her is going to grow up far faster than the canon timeline would permit, so she's going to have to be given some sort of boost by her kidnappers to either compensate for the actress' growth or to justify a teenaged actress playing her later (since teenagers don't age nearly as noticeably).
Sarah was held prisoner and had her memories alteredOne aspect of the show that's been conspicuously ignored is where was Sarah during the near year she was away. I think she was grabbed and spent a year being studied to figure out why she was able to conceive. She was then brainwashed to forget.
Helena has Kira's Healing FactorHow else is she still alive as of the season 2 premiere? And besides, she's practically Kira's biological aunt anyway.
Helena will do a Heroic SacrificeBecause Redemption Equals Death. I think they still intend for her to end up as an ally of the Clone Club, and the only way Sarah is going to forgive her for killing Amelia is if she dies to protect Kira.
Alison will kill Sarah (the woman in her musical)Or at the very least be there when she dies. The show seems to be setting Alison up to be seriously unhinged and also making this Sarah character to be a new friend of hers. Plus, one of the lines of a song of the musical Alison is in is "we will be together 'till the day that death takes us apart". Maybe it's foreshadowing?
Project LEDA is the reason why Sarah was able to have KiraSarah being fertile is of interest to the people of the DYAD, and Mrs. S is still hiding a secret.
Mrs. S killed Rachel's parents.The promo for "Governed As It Were By Chance" has a quick flash of a newspaper which says something about two Doctor Duncan's being killed in what looked liked a lab explosion. It will be revealed that Mrs. S was the one to cause it.
Donnie was only recently recruited to be Alison's Monitor.Donnie is pretty bad at being a Monitor based on what we've seen in Season 2. Also, Kristian Bruun has stated in interviews that he was told by the creators to play the torture scene as if he wasn't a Monitor. The reason: At the time, Donnie wasn't a Monitor. He was probably recruited during the time Alison left him at the couples retreat by himself. It would have been a perfect opportunity for Dr. Leekie to swoop in and recruit Donnie.
Alternately, Donnie being a monitor has to do with his college girlfriend.At some point in college Donnie and Alison broke up and Donnie started seeing another woman. According to Donnie, they stayed in contact after Donnie married Alison but then stopped and he (allegedly) doesn't know what happened to her. In reality, she's being held by the Dyad. Or she really is sick and the Dyad are Withholding the Cure. That's why Donnie got back together with Alison, to save the woman he really loved. While he acts like the devoted husband and father, he secretly resents Alison for building a "great" life with him when it should have been him with his lover for all those years.
Gracie's pregnancy/child is going to play a major role in future events.Given that a good amount of the main plot of season 2 is based around Sarah's ability to have Kira, it's not a far stretch that Helena's child that Gracie is carrying could play a huge role in the future storyline. It would be too major just to have her run off and never hear from her again.
The season 3 episodes will be named after quotes from The Island of Doctor MoreauGiven how important the book is now to the lives of the clones, plus the subtext it has in terms of the entire cloning experiment.
Sarah, Helena, and by extension Kira and Gracie's baby, are the result of a successful attempt to make a Super SoldierA Healing Factor would explain how Kira walked off the car crash, how Helena recovered from a gun shot to the chest so quickly and why they were the only fertile clones. It was also explain Sarah's Improbable Aiming Skills after literally minutes of practice and how Helena is such a terrifyingly competent assassin despite being trained to kill by nuns.
Season 3 will involve a Time SkipTo accommodate for the actresses of Kira and Charlotte as mentioned above, as well as to not make us wait for the results of Helena's and Gracie's pregnancies.
In Season 3, Rachel will get an Eyepatch of PowerIf she's still alive, that is.
In season 3, Helena's embryos will be used to save CosimaEmbryonic stem cells for the win.
Beth has a twin, who replaced her shortly before the time Maggie Chen was shotMultiple times throughout the series, it's been hinted by Paul or others that Beth has acted "oddly" before. Most viewers, if they suspect something, would suspect that the Beth that died wasn't actually Beth... but I'm going further with this theory. 1x03 is a very crucial episode to this theory, as it reveals that clones have identical fingerprints... yet the fingerprints of Sarah/Katja didn't match Beth! It's also never been stated whether Helena's prints match—she was wearing gloves in that episode. If Beth were merely another clone, then her prints would match Sarah/Katja. However, if she were a twin, there's a 1/2 chance that her prints would not match! Beth was then replaced by her twin (who believed she was a separate clone), and the twin proceeded to use Beth's identity, shoot Maggie Chen, and commit suicide with the intention that "Elizabeth Childs" would die. Meanwhile, the real Beth took the identity of (or, if dead, was identified as) her twin.