It's revealed that the blonde, Swedish, female scientist that has been seen throughout the series has the given name "Ellen".
Sheppard: I killed you.
Kolya: You shot me. There's a difference.
Sheppard: No – I killed you. Beckett confirmed it – you were dead.
They are referring to the season 3 episode "Irresponsible."
The capsule and the premise of the Humanoid median are very similar to the Stargate SG-1 episode "Scorched Earth," where a large ship had been sent across the Milky Way to search and terraform a planet for a Sulfur based life form, the Gadmeer, as well as all of the organisms of their homeworld and the knowledge of their race.
McKay: We need to get rid of it. Look, the energy signature that device is giving off is very similar to one we encountered on M1B-129. It can induce mass hallucinations.
McKay is referring to the Wraith device in the season 3 episode "Phantoms."
Sheppard: (referring to Dr. Parrish's alarming reaction to a plant) Oh god, Lorne warned me about this.
Sheppard is referring to a scene in the season 2 episode "Runner" in which Dr. Parrish has a similar reaction to the discovery of a rare plant.
At the end when Woolsey speaks to Ronon in the infirmary, Ronon's legs are over the blanket. In the next shot, his legs are under it.
Goof: When Ronon falls from the balcony and rolls down the steps, the illuminated Lantean letters on the first and second steps are upside-down.
This episode marks the death of Michael. This makes him the longest surviving Wraith at this point in the series, lasting 56 episodes and almost 3 years.
Goof: Near the beginning of the episode, after McKay and Sheppard attempt to climb up to the control room, McKay is seen with sweat dripping from his hair and has a sweat stained shirt. Shortly thereafter in his lab, his shirt is completely dry and his hair is dry and styled.
The scene of the transforming Wraith was not of Michael but a member of the Hive he brought to Atlantis in "Allies."
The Coalition now includes the Atlantis Expedition, the Free Peoples of Riva, the Tribes of Santhal, Latira, and the Genii. There are possibly more but it is not known.
It is stated that there have been, at the very least, 2 million human deaths in the five years since the Wraith were awoken by Sheppard in "Rising."
We learn that at least 12 Hive ships were destroyed during the Replicator War, bringing the number of Hive ships confirmed destroyed to 27 since the expedition arrived in the galaxy.
This episode bears some similarity to the Stargate SG-1 season one episode, "Cor-Ai", where it is Teal'c who is put on trial for the deaths he caused as Apophis's First Prime.
Sheppard: Look, even if you co-operate with the Wraith, there's no guarantee they're gonna keep their word. They may just kill all of you for being an inconvenience.
Past events supports Sheppard's statement. In the episode "Sateda" the planet that was culled, because Ronon brought the Wraith there when he was a Runner, was promised to be left alone if they turned him over to them if he returned. When Ronon and the team returned to this village Ronon was captured and turned over but the Wraith did not keep their promise and the village was destroyed.
McKay: Ronon's friend Tyre was pretending to be in league with the Wraith but really he was on our side so... he let us out.
McKay is referring to the episode "Broken Ties."
McKay: Ah, let's see. Uh, last time, Teyla was posing as a Queen, so, um... you know, she had us released.
McKay is referring to the episode "The Queen."
The Balarans were infected by Michael with the Hoffan drug and most of the people died. The survivors left Balar and were taken in by villagers on another planet.
Nitpick: When the Wraith are waiting by the gate with the prisoners one of them comes up and whispers something into the commanders ear but it has been strongly pointed out several times that the Wraith are telepathic and can communicate thoughts to one another, so why bother whispering?
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Futuristic, space travel, Time Travel, alien technology, planetary explorers