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Best Episode (Atlantis Season Three)
  • Sateda
  • Common Ground
  • The Return, Part 2
  • Tao of Rodney
  • Sunday

Best Sheppard Moment
  • Hanging onto the hull of a Wraith hive ship in his F-302, Sheppard debates whether or not to trust Michael to help him rescue his friends and stop the hive. ("No Man's Land")
  • John risks his own life when he breaks quarantine to support an ailing Elizabeth Weir, encouraging her to fight the nanites taking over her body. ("The Real World")
  • Sheppard is captured by Commander Kolya, who uses a Wraith to slowly drain the life out of him -- until the two prisoners form an alliance and escape. ("Common Ground")

Best McKay Moment
  • McKay works alongside his estranged sister Jeannie in an attempt to save two realities, and tries to reconnect with her. ("McKay and Mrs. Miller")
  • An Ancient device turns McKay into a highly advanced human, vastly increasingly his intelligence and giving him superhuman abilities. ("Tao of Rodney")
  • Facing death after being altered by an Ancient device, Rodney spends his final hours attempting to ascend -- and showing his friends what they mean to him. ("Tao of Rodney")

Best Teyla Moment
  • With Atlantis under Ancient control and her friends returning to Earth, Teyla says farewell -- telling Sheppard that their paths will cross again. ("The Return, Part 1")
  • When the team finds a Wraith Queen inside a facility at the ocean's floor, Teyla tries to telepathically access her mind -- only to be taken over by the powerful Queen. ("Submersion")
  • Teyla uses her telepathic ability to trick a Wraith Queen into thinking she has control over Teyla, stopping her ship's self-destruct and luring the Queen into a trap. ("Submersion")

Best Ronon Moment
  • Captured and handed over to the Wraith, Ronon is returned to the ruins of his homeworld and made a Runner once again. ("Sateda")
  • Trapped on Sateda as a Runner again, Ronon challenges the Wraith commander orchestrating his hunt to come down off the hive and fight him personally. ("Sateda")
  • Ronon says goodbye to his friends in Atlantis after the Ancients return and take over the city -- refusing to leave the galaxy until every last Wraith is dead. ("The Return, Part 1")

Best Weir Moment
  • Infected with Replicator nanites threatening to kill her, Elizabeth dreams that she is back on Earth -- a fragile psychiatric patient who dreamed up Atlantis and the Stargate. ("The Real World")
  • With help from her friends, Elizabeth fights against a nanite-induced hallucination of another life and makes her way back to her real life on on Atlantis. ("The Real World")
  • When Sheppard is captured and tortured by Kolya, Dr. Weir refuses to back down while negotiating his release. ("Common Ground")

Best Beckett Moment
  • After his retro-virus successfully turns a Wraith crew into humans, Beckett does everything he can to help them survive on a new planet -- soon realizing that the Wraith haven't entirely lost their memories. ("Misbegotten")
  • Dr. Beckett fights to save Elizabeth Weir when she is infected by Replicator nanites, coming up with a brilliant plan to distract the nanites and give her mind a fighting chance. ("The Real World")
  • Carson acts against orders to save a patient, putting his own life on the line to surgically remove an explosive tumor -- and is killed in the line of duty when it detonates. ("Sunday")

Best Team Moment
  • Having relocated back to Earth, the members of the former Atlantis expedition reunite for dinner to talk about old times. ("The Return, Part 1")
  • Defying orders and reuniting in the Pegasus Galaxy, Sheppard and his team rescue Woolsey and General O'Neill from the Asuran Replicators and retake Atlantis. ("The Return, Part 2")
  • Under attack from the Asurans, the Atlantis team works together to escape the enemy weapon satellite and fly the city off the surface of Lantea. ("First Strike")

Best Alien Race (Season Three)
  • The Asurans ("Progeny")
  • The Ancients ("The Return, Part 1")
  • Herick's race ("The Ark")

Best Individual Villain
  • Oberoth ("Progeny")
  • Acastus Kolya ("Common Ground")
  • Michael ("Vengence")

Coolest Ancient Technology
  • Satellite game ("The Game")
  • Ascension machine ("Tao of Rodney")
  • City stardrive ("First Strike")

Coolest Alien Technology
  • Anti-Replicator guns ("The Return, Part 2")
  • The Ark ("The Ark")
  • Asuran satellite weapon ("First Strike")

Best SG-1 Crossover
  • Richard Dean Anderson as Jack O'Neill ("The Real World")
  • Richard Dean Anderson as Jack O'Neill ("The Return, Part 1")
  • Richard Dean Anderson as Jack O'Neill ("The Return, Part 2")
  • Robert Picardo as Richard Woolsey ("The Return, Part 2")

Best Guest Star
  • Kavan Smith as Major Lorne ("No Man's Land")
  • Robert Davi as Acactus Koyla ("Common Ground")
  • Christopher Heyerdahl as Todd ("Common Ground")
  • Kate Hewlett as Jeannie Miller ("McKay and Mrs. Miller")
  • Michael Beach as Abraham Ellis ("First Strike")