Stargate Atlantis: Season Two

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Summary

This article covers the episodes of the spin-off Stargate Atlantis as it crosses stories with Stargate SG-1 or as it impacts the mythology of the Stargate universe.

Précis

The Atlantis Expedition Team begins their second year in the Ancients' city-ship as the war with the Wraith takes on interesting twists, including the discovery of advanced technology left behind by the Ancients.

Season Two

2.01 "The Siege Part 3"

Col. Steven Caldwell, commander of the Daedalus
Daedalus lands on Atlantis
File:Atlantis-201.jpg
Atlantis is seemingly destroyed to fool Wraith

From SciFi.com Official Episode Summary:

The Wraith assault on Atlantis rages on. In the midst of the chaos, Dr. Beckett treats Lt. Ford, who has been rescued from a near-fatal encounter with the alien invaders. Ford's abnormally quick recovery, however, leaves the doctor suspicious. He worries that the Wraith who attacked Ford might have injected the young officer with a harmful enzyme, causing unpredictable long-term damage.

Meanwhile, far above the planet and surrounded by Wraith, Maj. Sheppard faces seemingly certain death — until he is rescued by Earth's newest and most sophisticated space battle cruiser, the Daedalus. Commanded by Col. Steven Caldwell, the Daedalus has completed its long journey to the Pegasus galaxy just in time. With its help, the Atlantis team defeats the Wraith's first assault on the city.

Their victory, however, is short-lived. The next wave of the Wraith onslaught — an entire fleet — is bearing down on Atlantis. With a little over a day before the new attack, Dr. Weir realizes that even the Daedalus will be no match for the Wraith's redoubled forces. The team's only hope is a drastic plan devised by Dr. McKay — but the complicated technology it requires might take too long to perfect.

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2.02 "The Intruder"

Daedalus returning to Atlantis in hyperspace
Asgard Hermiod
Daedalus and errant F-302 fly toward a sun

From SciFi.com Official Episode Summary:

Drs. Weir and McKay and the newly promoted Lt. Col. Sheppard are en route from Earth to Atlantis on board the Daedalus. Their first visit home has been emotionally draining, and they are looking forward to resuming their lives in the Ancient city.

Soon after they cross into the Pegasus galaxy, however, a scientist is electrocuted in the Daedalus's computer room. McKay first believes that faulty circuitry is to blame, but then a second scientist is killed while investigating the problem. Now convinced that the deaths are no accident, McKay convinces Col. Caldwell, commander of the Daedalus, to drop the ship out of hyperspace until the murderous saboteur can be found.

With the help of the ship's Asgard advisor, Hermiod, McKay quickly discovers that the saboteur isn't a person at all — it's a Wraith computer virus. It seems to possess some form of artificial intelligence, allowing it to predict the actions of its human opponents and rewrite itself in response. Unless those on the Daedalus can stop it, it will fly the ship straight to the Wraith, giving them access to all the advanced human and Asgard technology aboard.

When McKay attempts a full system shutdown, the resilient virus responds by flying the ship straight toward the coronasphere of a nearby star. The route will not destroy the ship, but the intense radiation will kill everyone aboard, freeing the virus to continue its mission without interference. As they zoom toward the star, Sheppard, McKay and the others know they will have to find a solution quickly if they want to see their new home again.

NOTE: It is possible that this trip from Earth to Atlantis onboard the Daedalus is the ride which Daniel Jackson missed when Vala Mal Doran attached herself to him with the Kor Mak bracelets in the episode, 9.01 "Avalon Part 1".

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2.13 "Critical Mass"

Agent Barrett briefs Gen. Landry and Dr. Lee on the Goa'uld threat to Atlantis
Dr. Lee explains communication relay from Earth to Atlantis
Col. Caldwell unknowingly has become a Goa'uld host

From SciFi.com Official Episode Summary:

On Earth, a galaxy away from Atlantis, Gen. Landry receives intelligence that The Trust, a group of conspirators controlled by the evil Goa'uld (8.14 "Full Alert"), have learned of the Ancient city and sent an undercover operative there to plant a bomb. Details are sketchy, but any use of Atlantis's Stargate to dial Earth will somehow trigger the explosion.

The moment that Earth relays this news to Atlantis, Dr. Weir orders both the Stargate and the city's main power source, a ZPM, shut down. She also orders the absent starship Daedalus to return, because the bomber might be trying to escape aboard it.

In the midst of this intense search for both bomb and bomber, the city's distress beacon activates. Before McKay can shut it off, it catches the attention of two Wraith cruisers, who head straight for Atlantis. If they discover that the city still exists, they will attack immediately. To prevent such a catastrophe, McKay prepares to reconnect the ZPM and use its power to cloak the city from view.

Suspicion is consuming the city. McKay suspects that Lt. Cadman, a demolitions expert, is the saboteur. Weir suspects Dr. Kavanagh, a disgruntled scientist. For his part, Kavanagh suspects Dr. Zelenka, who is off-world on a conveniently timed mission. Weir's suspicions carry the most weight, however, so the investigation's focus settles on the prickly and defensive Kavanagh.

Then McKay discovers that no actual bomb exists. Instead, the saboteur has removed the failsafes from the ZPM, so that it will overload in a massive explosion as soon as it emits any significant amount of power. The saboteur has been trying to provoke them into dialing Earth or cloaking the city — either of which will cause an overload.

But the Wraith are closing in. In desperation, McKay shuts down as many secondary systems as possible and activates the cloak. As the power usage levels inch toward critical, Weir considers torturing Kavanagh for answers. Atlantis teeters on the brink of destruction, though whether it will come from without or from within remains to be seen.

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--DeeKayP 07:33, 14 June 2006 (PDT)