"Hot Zone" reveals that Zelenka has been given the ATA gene therapy to enable him to operate Ancient technology, but the therapy had no effect on him. Season 2's "Duet" shows Zelenka off-world for the first time, where he needs to save McKay and a soldier from being captured in a Wraith dart. Following a major dispute about an experimental Ancient power generator in "Trinity", McKay apologizes to Zelenka when the experiment causes the death of a scientist. McKay saves Zelenka from certain death in "Tao of Rodney" and later apologizes for so often putting him down, admitting that Zelenka is "a brilliant scientist and a decent human being". Zelenka last appears in the series finale of "Atlantis", "Enemy at the Gate", where he implements a wormhole drive that sends the city of Atlantis from the Pegasus Galaxy to Earth within seconds.