The so-called Lanteans of Stargate: Atlantis are not the original builders of the Gate network.Draga, the winged lizard-like alien discovered in Stargate: Infinity, is not remotely humanoid, but is called an "Ancient". This is not because Infinity was deprecated by Atlantis. No, in the decades between the two shows, the name was simply reassigned to a new unknown, and presumably more fundamental, race.
Pegasus Stargates cause brain damage.The characters on Atlantis often seem to be a few sandwiches short of a picnic. This especially applies to Ronon, who spent seven years constantly traveling from world to world. The only exception is Caldwell, who has his own starship and almost never uses a Stargate.
Pegasus Stargates infect people with Pegasus LogicThis is, naturally, morally superior to Earth logic. Whenever a Hero is captured, the Others come up with a rescue plan. Caldwell is treated as the bad guy because he doesn't want to sacrifice his thousand Red Shirts and the ONLY Tauri ship in the Galaxy just to rescue one man. But Pegasus Logic works in its own galaxy. Hero always gets rescued, and it doesn't matter how many Red Shirts die.
Dr. Keller is a Wraith.On Atlantis, first we see Ellia, a Wraith raised by a human who desperately wants to become human herself. She apparently dies. Then we see the Atlantis crew transform a Wraith into a human, amnesiac but with a complete life story made up by the crew. Then we see a new doctor appear on Atlantis that we've never seen before, who looks exactly like a human version of Ellia. Hmm.
Amelia Banks is a Replicator.In the episode Lifeline, we see a female Replicator technician. By Quarantine, an identical woman is employed in a similar capacity on Atlantis. Coincidence, or Replicator infiltration?
Michael is the Wraith scientist who gave Teyla and the Athosians Wraith DNA hundreds of years agoCrossing species together seems to have become Micheal's major M.O., and he's especially interested in Teyla and her baby. He's established to be a brilliant biological scientist, and being a Wraith he could easily be old enough to have been around back then. The fact he's never brought it up in conversation can be chalked up to the memory wipe the Atlantis team gave him when they experimented on him.
Todd is the Wraith scientist who gave Teyla and the Athosians Wraith DNA hundreds of years agoMichael didn't show any interest in genetic engineering until he was himself a victim of it, while Todd on the other hand seems one of the oldest and most reasonable Wraith in the Galaxy. Not to mention he's also a scientist who has fluctuating standing within the Hive. By making feeding more efficient, he was going to solve the problems he's been trying to solve in Season 5. It would also explain his clear interest in Teyla, and knowledge about her abilities (Episode: The Queen).
The Wraith's Villain Decay is a result of the food shortage.With fewer humans around to feed on, they aren't getting enough nourishment to maintain their Healing Factor that made them so hard to kill in the first place. The link between feeding and Healing Factor is demonstrated in Todd's introductory episode. During the escape sequence, the Wraith that will eventually be known as Todd acts as a bullet sponge. He feeds more than any single Wraith we've ever seen, going so far as to drain Sheppard repeatedly, despite draining to death at least one Genii from every squad they encountered.
Martin Gero and David Hewlett are the same person.They're both Canadians who have written and directed their own movies, and Gero seems to identify strongly with the character Hewlett plays. They even look reasonably similar - any differences could just be make-up and hair styling. Yes, we've seen them together on a parody video, but we've also seen Hewlett play two characters in the same scene.
Todd is suffering from PTS/Stockholm Syndrome.Is it a coincidence that the only Tau'ri-sympathetic Wraith character so far was imprisoned for X number of years by humans beforehand? Either he's very forgiving (never seen to be a Wraith trait), or there's some serious mental trauma going on under that mop of his.
Halling is Todd in disguiseIn a similar vein to the 'Dr. Keller is a Wraith' and 'Todd gave the Athosians their Wraith DNA' WMG's above, Halling is in fact Todd in disguise. After all, what sort of scientist wouldn't want to monitor his experiment? He's just using makeup like the Wraith we see on Earth in Vegas to look like he's not a Wraith at all.
Ronon is part NietzchienRonon looks awfully similar to Tyr Anasazi. Both of which are physically superior and have advanced fighting skills. Explains how Ronon can face dangerous adversaries like gouald, wraith, hybrids and Tealc.
The wraith are actually the same species as Morbius the living vampireIts never fully explains how the iratus bug evolved into the wraith and neither does it make a whole lot of sense seeing as their should be all sorts of iratus hybrids. Its well known those lazy ancients are responsible so it was probably a whole host of chimera experiments designed to make a life form either more resistant to the plague or diagonal on the human evolution chain. A lot of radiation and bat DNA mixed with the magic ingredient if Iratus DNA and hey presto- wraith.
Rodney is DecadeHe destroyed worlds, uninhabited, but still worlds and he travels to various worlds. He just hasn't discovered the Decade Driver yet.
Had the show not been canceled, Todd would have become a regular.The original Season Five finale did not have a direct threat to Earth, but rather had Kenny attacking Atlantis after overthrowing Todd. After destroying Kenny's fleet, Todd would have had nowhere else to go. He would have undergone Keller's gene therapy and ended up on Sheppard's team.
Genghis Khan had the ATA geneIt's been theorized that because Genghis Khan got so much action, approximately one percent of earth's population is descended from him. If memory serves, that's about the same as the percentage of people who have the ATA gene.
"Home" was the last actual episodeThe rest of the series was just an illusion created by those energy beings.
"Progeny" was the last actual episodeThey are still in a holding cell on Asuras, being mind-probed.
Carson used to be a drug addictWhen Rodney is going through withdrawal he states "you have no idea of the agony I'm going through." Carson replies "Oh, I have an inkling." I don't think this was ever referenced again.
Rodney's allergy to citrus came from a bad experience and has no allergyAlternate timeline, and much happier, Rodney does love lemon chicken, whereas main timeline, and very unhappy, Rodney is afraid of a lemon
Scotland has become an independent country in the Stargate Verse timeline by the time Atlantis begins.Carson Beckett, the only Scot we see on the base, is wearing a Scottish flag patch rather than the UK flag patch you'd logically expect him to be wearing - unless Scotland is no longer part of the United Kingdom. Otherwise, him wearing that patch makes about as much sense as an American team member wearing their state's flag as a patch, or a Canadian wearing the flag of their home province. It's even relatively plausible, considering the fact that the Scottish independence movement is a very real thing.
The unidentified gay male supporting character is Major Lorne.Just a hunch.
Mensa is aware of the Atlantis Chapter of MensaIt's a shame they can't host an RG, though, due to the secrecy. All that open space for a convention.
Laura Cadman is gay.When Laura Cadman's mind is stuck inside Rodney McKay's brain, she insists he turn up to a dinner date, keeps giving him advice on romance, and eventually takes over his body and passionately kisses his date. That seems to suggest that she's attracted to his date herself. Her pursuit of Carson is done purely to annoy McKay — Carson's later relationship with her doesn't go beyond a couple of dinner dates. Even McKay seems to recognize this. He irritably says that he doesn't need her to be his "Cyrano". The Cyrano from the play was in love with Roxanne himself.
The ATA gene therapy isn't given to everyone at the SGC.Because of the problems with accidentally activating ancient equipment when simply cataloging it.
When Ronon Dex "dies" in "Enemy at the Gate" he has a hallucination about being on a strange world.Where he is the leader of a tough group of Dothraki. He meets a nice Khaleesi. The witch who "kills" him is an extension of the Wraith who brings him back.
They're going the have a devil of a time with Atlantis being on EarthBecause all the gate traffic will reroute to the more updated version of the gate - in Atlantis. There's going to be a lot of confused SG teams coming in...
The series Life After People is post-culling EarthIn the series you don't find out what happened to humans. A culling makes sense. The Wraith finally found Earth in this reality. And what a party they had!
Michael isn't dead.Or more correctly he's dead, but he's left a clone behind that will activate after a certain period of time. The original Michael has left a message warning the clone Michael to find out what happened to him first (so the clone doesn't repeat that mistake,) and when the time is right, emerge to cause as much chaos as he possibly can.