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I haven't watched every Stargate: Atlantis episode, but I've watched quite a few from the later seasons and have been watching some lately from an earlier season. One thing that really confuses me is in the three part episode "The Siege" from an earlier season, the Wraith some how know about Atlantis and are attacking it. Then they pretend to blow up Atlantis and all the Wraith leave...

Later in the series the Atlantis team has help from a lone Wraith, who Shepherd met while imprisoned. This Wraith eventually learns of where Atlantis is. In those seasons it sounds like Atlantis is a secret to the Wraith, which is why they are never under attack. But clearly in the early episodes I mentioned the Wraith knew all about Atlantis and just decided to leave. Shouldn't they know about Atlantis later on too? Why don't they go back and attack? And also why did they just leave without checking the sea around Atlantis? Wasn't the whole point of not doing a self-destruct was their fear that the Wraith would stick around and check the rubble?

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Atlantis' location (in space) is known to the Wraith. I do not believe they know the gate address.

The Wraith also know that Atlantis is capable of space flight.

When they discovered they were fooled in the Siege, they believed the city had then been moved - it wasn't worth going to check, because whatever ship went to check WASN'T involved in feeding. The 'stock' of humans was low...too low to support all the awakened Wraith.

None of the wraith were willing to travel to a planet where they were certain the city would no longer be (because who'd be silly enough to decloak and stay there, when they could just fly away?) - they'd get less food, waste energy, and be in a worsened position relative to their peers.

The Wraith assumed the Atlantis expedition (who appear the same as the Lanteans, recall) would have flown away, not knowing the expedition couldn't do so.

edit - it's also possible that they do know the gate address, but also know about the iris-like energy field, and assume it'll be up.

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    For 20% of the show's history, Atlantis's location in space was most certainly not known to the Wraith. – Lightness Races in Orbit May 17 '11 at 20:24
  • @LightnessRacesinOrbit but why would the Wraith leave the city alone for the 10,000 years it was submerged and dormant. They most certainly knew it's general location and even if they knew only a few Ancients had escaped (if anyone) why wouldn't they either covet the more advanced technology or act to prevent any return by their enemy by finishing the destruction of Atlantis in all that time? – John LA Oct 8 '19 at 9:43
  • @JohnLA A good question (though seemingly unrelated to my comment) and one worth asking as such – Lightness Races in Orbit Oct 8 '19 at 10:42
  • @LightnessRacesinOrbit - guess I took the original question more literally and the thought crystalized because of your comment. I guess I will post it, thanks. – John LA Oct 9 '19 at 5:49
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In addition to other answers, talking about the use of shield and cloak during the season 1 finale (The Seige), the City of Atlantis changes location at least once during the show.

In the season 3 finale (First Strike) the city is attacked by the Asurans, and the only escape is to flee by taking the city into space. By the second episode of season 4 (Lifeline), they have made a new planet their home. IIRC, the new planet has two moons instead of one.

In part, this explains why the Wraith didn't know where it was in seasons 4 and 5 - it had physically moved.

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    @Jeff so true, I have always wondered why didn't the Humans told wraith location of earth in the Ori galaxy ? Swallowed are the ORI ? – ShrekOverflow Nov 29 '15 at 16:05
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The wraith don't know much about Atlantis really, at the end. A few wraith know where Atlantis is, but they hold the secret so they can exploit Atlantis for their own purposes. Also, at the end of the series where they know the most, the wraith are practically in an all out civil war, basically removing the coordination that would be required to take over Atlantis.

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You missed the episode where they moved the city to a different planet. And several subsequent episodes where there were mentions that they were now on a different planet.

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