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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
Stargate Atlantis
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.
  • The remnant Ancient technology encountered by the SGC has appeared to follow multiple aesthetics, some of them seemingly incompatible with the very-human survivors of the Lantean warship Tria. This is because Lantean civilization lasted for several million years, and underwent many ups and downs and technological cul-de-sacs.
  • More likely, Draga is actually a Furling, and just too embarassed to admit it.

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.
  • Despite having brilliant scientists, it seems like the Expedition can't so much as turn on an Atlantean iPod without someone losing an eye.
    • That was because the Atlanteans never built an iPod that didn't poke out people's eyes. Of course, the Ancients probably used stargates all the time.
  • Warning: Gate travel may be hazardous to your health.

Pegasus Stargates infect people with Pegasus Logic

This 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.
  • That also suggests that Halling, the leader of the Athosians, is also secretly Todd, the leader of the Wraith.

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 ago
Crossing 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 ago
Michael 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).
  • And was punished for his experiments by being handed over to the Genii.
  • Brilliant! It fits so well. It always pissed me off that Humans treat Todd like Gryffindors treat Slytherins, but, Todd keeps coming back for more!
  • Why don't Wraith have names? How can the Queen order wraiths to work the darts, the artillery, the engines, the shields etc. They could have Hand Waved it with puny mortals can't speak wraith.

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.
  • I do believe this is canon.

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 disguise
In 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 Nietzchien
Ronon 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 vampire
Its 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 Decade
He 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.
  • Todd had already undergone the gene therapy before the end of the show, in the episode where one of his hive ships has a tumor that causes it to tear itself apart. But yeah, they were really hinting at the fact that in season six Todd would be a regular. Oh, What Could Have Been...
Genghis Khan had the ATA gene
It'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.
  • Genghis Khan was an Ancient!

"Home" was the last actual episode
The rest of the series was just an illusion created by those energy beings.
  • Rodney said it himself, "How do we know this isn't a double fakeout?"

"Progeny" was the last actual episode
They are still in a holding cell on Asuras, being mind-probed.

Carson used to be a drug addict
When 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 allergy
Alternate 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.
  • Scots can be very independent-minded, it wouldn't be surprising at all if he had some Scotland flag patches made for himself to wear instead of the UK ones, and damn the regs.
  • Possible. Scotland had a referendum in 1979 that would have led to at least a degree of independence if there hadn't been a rule about "minimum turnout" needed for the vote to be valid. Maybe in the SG-verse the opponents of the referendum failed to insert the rule, limited independence happened, then the rest of the 80s (in which Scotland bore the brunt of the economic turmoil and got little of the benefits as in real-life) made it possible for full independence. This is science-fiction after all.

The unidentified gay male supporting character is Major Lorne.
Just a hunch.

Mensa is aware of the Atlantis Chapter of Mensa
It'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.
  • She could also be bisexual — she was pursuing Carson for real, but she also found McKay's date plenty attractive.

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.
  • Maybe people who refuse the treatment are given a bonus because they don't get to play with all the neat toys.

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 Earth
Because 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...
  • It is using the correct protocol (taking over like a DHD) alternatively it is a diffrent system and you need an 8 symbol gate address.
  • The IOA probably loved it. Atlantis is an IOA run facility, Cheyenne Mountain was IOA supervised, but still US Military controlled. I'm just surprised they authorised it being sent back to Pegasus in the book series, it would have made far more sense for them to order it relocated to mid-Pacific or mid-Atlantic (out of US waters and airspace) and run it free and clear of US military intervention. The IOA were, quite reasonably when you think about the wider implications, never entirely comfortable with the US having such a stranglehold on off-world travel and resources.
  • If the IOA didn't love it, then they could just take the control crystal out of Atlantis's gateroom and take the Atlantis gate offline.

The series Life After People is post-culling Earth
In 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.

The Wraith don't actually have names.
It's not just a joke; they literally don't have names in the same way we Humans think about it. They're a highly-telepathic race, able to communicate mind-to-mind. They don't need spoken names to distinguish individuals from one another; they just know.
Stargate SG-1WMG/Live-Action TVStargate Universe

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