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"Todd" (Christopher Heyerdahl) informs Atlantis that a group of Wraith have multiple ZPMs and they plan to use one of them to power a new super Hive Ship. "Todd" urges the expedition to destroy it, but when the team reaches the hive, they realize that the ZPM has already made the ship far more powerful than expected, and causes significant damage to Daedalus before jumping into hyperspace.
In the season finale (also the series finale), "Enemy at the Gate", Todd the Wraith alerts Atlantis to the fact that an underling wraith possesses a Hive Ship powered by a ZPM. In the process of trying to retrieve the ZPM and disable the Hive, the Daedalus is crippled, and the hive suddenly jumps away without destroying the Daedalus.
The team investigates mysterious happenings on board a Wraith Hive, where Todd and his crew are suffering from a disease, just to find that since Wraith ships are organic, the ship has the disease as well. It's revealed they got this disease when they tried Keller's gene therapy which did work, but left them with a weakened immune system.
The Wraith is imprisoned and Sheppard starts to interrogate him after he named him Bob, but he keeps silent. Meanwhile, the Wraith Hive-Ships drop out of hyperspace as predicted, and Grodin powers up the satellite. McKay watches from the cloaked Puddle Jumper as the energy beam from the weapon successfully slices through and destroys one Hive-ship.
In 2009, an enhanced Wraith Hive Ship heads to Earth to feed upon the human race. With Earth ships unable to defeat the ship, Atlantis leaves the Pegasus Galaxy and returns to Earth. After destroying the Wraith ship, Atlantis lands in San Francisco Bay, overlooking the Golden Gate Bridge in the episode "Enemy at the Gate". [60]
The Wraith-enzyme allowed Ford to awake immediately after rematerializing on board a Wraith-hive ship, from where he escaped only to build up a small strike force of young men following his suit by informing them about the benefits of the Wraith-enzyme. Ford asks the Atlantis team for help in destroying an entire Wraith Hive-ship, but the ...
In the Atlantis series finale, Beckett flies the city from M35-117 back to Earth to defeat a super Wraith Hive Ship. Beckett pilots the city in battle against the hive ship, but is unable to defeat it. The city is nearly destroyed, but is saved at the last moment when Sheppard manages to destroy the hive ship from the inside with a nuclear weapon.
To keep the Wraith from using the facility again, Sheppard has Teyla crash their captured hive ship into it, destroying both. Todd is allowed to go free and the team returns to Atlantis where the situation makes Teyla finally understand why she can't go out on missions anymore and risk her baby.