The best episode directed by William Waring is "The Pegasus Project", rated 8.833/10 from 18 user votes. It was "written by Brad Wright". "The Pegasus Project" aired on 7/28/2006 and is rated 0.1 point(s) higher than their second highest rated, "Common Ground".
Daniel and Vala travel to Atlantis in search of Merlin's anti-Ori weapon, while Sam, and Mitchell join forces with Dr. McKay to lock out the Ori supergate.
Director: William Waring
Writer: Brad Wright
Colonel Sheppard finds himself the prisoner of a Genii commander, along with a desperately hungry Wraith who has been separated from his hive.
Director: William Waring
Writer: Ken Cuperus
As the Ori invade the Jaffa planet Chulak, Vala and Daniel must deal with their leader: Vala's young daughter, rapidly aged by the Ori to serve their purposes.
Director: William Waring
Writer: Robert C. Cooper
SG-1 hatches an elaborate plan to try and capture Adria, using Vala as bait.
Director: William Waring
Writer: Alex Levine
The team tries to relax during a mandatory day off, until an explosion leaves three people dead -- and reveals that one scientist is a walking time bomb.
Director: William Waring
Writer: Martin Gero
While MacLaren, Carly, Trevor, and Philip work with another traveler team to protect a child important to the future, Marcy takes measures to remember her past life – but uncovers more than she bargained for.
Director: William Waring
Writer: Brad Wright
MacLaren is kept on a tight leash after the Director orders an assassination.
Director: William Waring
Writer: Amanda Smith-Kolic
Daniel Jackson is exposed to a lethal dose of radiation while visiting an alien civilization that is building a weapon of mass destruction.
Director: William Waring
Writer: Robert C. Cooper
SG-1 finds a genetically advanced Goa'uld-human hybrid created by Anubis, and returns him to Earth for study. But even keeping him alive may not be worth the risk.
Director: William Waring
Writer: Alan McCullough
A mysterious drone crashes into Atlantis, indicating that the Replicators may have found the city. But when Elizabeth Weir appears, the team realizes that the probe is just a part of a bigger mystery.
Director: William Waring
Writer: Brad Wright
The S.G.C. is put under quarantine after a mysterious infection leaves a Russian officer in the infirmary -- but the disease may not be a disease at all.
Director: William Waring
Writer: Paul Mullie
When the team meets Simon, a homeless man with a startling history, they’re led down a path that leads directly to the very first traveler.
Director: William Waring
Writer: Jason Whiting
Sheppard and McKay discover that their competitive video game has been controlling a planet of real people, who now stand on the brink of war.
Director: William Waring
Writer: Carl Binder
The team finds their former Wraith ally's hive ship drifting in space, which leads them to a secret project that could turn the tide of a civil war.
Director: William Waring
Writer: Alan McCullough
Colonel Sheppard is captured by the inhabitants of a generational ship and their beautiful leader, who wish to use his ability to use Ancient technology for their own ends.
Director: William Waring
Writer: Paul Mullie
While being evaluated by the International Oversight Advisory, Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Meanwhile, Lt. Colonel John Sheppard is captured and tortured by an enemy he thought he'd killed several years ago: his sworn enemy, Genii Commander Acastus Kolya.
Director: William Waring
Writer: Paul Mullie
The team finds an impoverished world enslaved by a Goa'uld underlord, but their plans to free it may be compromised when Jonas experiences unexplained visions of the future.
Director: William Waring
Writer: Joseph Mallozzi
The inhabitants of Atlantis begin to suffer ill effects when the planet's whale population begins migrating to the island city, bringing an unexpected harbinger of doom.
Director: William Waring
Writer: Brad Wright
When a group of Ronon's people enlist the team's help in raiding a Wraith weapons facility, Ronon reconsiders whether his future lies in Atlantis or with his friends.
Director: William Waring
Writer: Paul Mullie
A duplicate of Colonel Carter seeks help from Stargate Command in defeating the Replicator Fifth, who she claims has found a way to counter the Asgard's new weapon.
Director: William Waring
Writer: Peter DeLuise
MacLaren has to find a lone bomber who kills a newly arrived group of travelers.
Director: William Waring
Writer: Ashley Park
Dr. Carson Beckett is called in to help a team investigating a lab that once belonged to Michael Kenmore. But soon, they realize that a group of experiments that even Michael couldn't control are hellbent on killing the team.
Director: William Waring
Writer: Paul Mullie
When a mysterious alien organism takes Dr. Jennifer Keller as its host, the newly revived Dr. Carson Beckett and the crew desperately search for a serum to save her from the evolving intruder before it can infiltrate Atlantis. In the meantime, Richard Woolsey officially joins the team, having been chosen as Colonel Samantha Carter's replacement to lead the Atlantis expedition.
Director: William Waring
Writer: Paul Mullie
Dr. Jennifer Keller is kidnapped by a runner named Kiryk. While Dr. Rodney McKay and Ronon Dex tracks them, Kiryk takes Keller to a seriously injured young girl. She must do it fast, since the Wraith have found him, and are hunting them down.
Director: William Waring
Writer: Carl Binder
Everyone is shocked when a member of the crew is found dead from a gunshot wound. While at first glance it appears to be suicide, the gun is nowhere to be found. The crew is confined to quarters while a search is performed and when the gun shows up in Col. Young’s quarters, he becomes the number one suspect.
Director: William Waring
Writer: Alan McCullough