Pilot episode. A full writeup is available.
Commander William Boone tracks his wife's murderer, determined to find out if the American Companion Da'an or the underground resistance ordered her execution.
In the end, Boone discovers that it was Agent Sandoval who hired a hit man (Judson Corr) to kill his wife, in order to ensure his loyalty to the Companions. Sandoval even had his own wife committed to a mental asylum to keep her out of the way. This isn't exactly a surprising ending considering what a jerk Sandoval is throughout the entire series, although since it's only the second episode we don't know him too well yet.
A young woman (played by Emily Hampshire) becomes a pawn in a power play between the Companions and a charismatic religious leader (Peter Krantz) when her hands are "regenerated" by Taelon technology.
Boone had talked the woman, Julie Payton, out of committing suicide and presented her case to Da'an. When her hands were successfully regenerated, Julie came to believe that the Companions were messengers of God, and joined the newly formed Church of the Companions. Alas, her new hands began to deteriorate, and she turned to Travis Murray, founder of the Church, for help.
Not trusting Murray for a second, Lili and Boone broke into his headquarters and rushed Julie out of the building. Boone and Lili arranged for her to appear on a top-rated talk show, where she announced to the world that although the operation had failed, she still considered it a miracle. This wasn't quite what Boone and Lili were hoping for her to say, and despite the failure of the experiment, membership in the Church rapidly increased. Thrilled, Da'an complimented Murray on his success.
A serial killer (Richard McMillan) programmed with a CVI tries to kill Da'an when he enacts an ancient Taelon myth about good conquering evil.
Boone's double-agent cover is put to an extreme test when a long-lost love (Colette Stevenson) resurfaces in his life, claiming to be working against the Companions.
Float Like a Butterfly
Boone and Lili are summoned to the small Amish town of Paradise to investigate the mysterious (almost alien?) deaths of several of its citizens.
Jonathan Doors comes out from hiding, launching a media attack against the Taelons, leaving Boone to deal with the ramifications.
When Lili's shuttle is stolen by a friend whose mission to Mars has been cancelled by the Taelons, Boone has to help the Resistance make the most of the stolen shuttle without breaking his orders to find it for the Companions.
Dr. Larry Clark falls under the control of his skrill when Boone informs him that his laboratory will be shut down.
Live Free or Die
Da'an is held for ransom by a group of renegade soldiers who claim the Taelons sacrificed their unit during radical bioengineering experiments.
The Scarecrow Returns
The Resistance does battle with an alien probe that may be studying Earth.
Sandoval reunites with his wife when the implant in his brain degenerates, setting him free from Taelon mind control but endangering his life.
The Secret of Strand Hill
An ancient Taelon grave in Ireland reveals that the Taelons had been planning Earth's occupation for centuries.
A Taelon experiment to create a new hybrid warrior ends in disaster when an ancient alien evil is brought to Earth.
If You Could Read My Mind
A gifted Russian psychic becomes a target for assassination because of her knowledge about the Taelon occupation of Earth.
The Wrath of Achilles
Da'an saves Lili's life after a shuttle crash caused by a computer virus which threatens the Taelons' entire existence on Earth.
The Devil You Know
When the Taelons mastermind the sale of an illicit weapon to trap Resistance leader Jonathan Doors, Lili's estranged father (Doug Lennox) is part of the scheme.
Law & Order
William Boone and Agent Sandoval defend the Taelon scientist Rho-ha, who is ordered to stand trial for murder.
Through the Looking Glass
The Taelons introduce interdimensional travel to human customers for the sinister purpose of harvesting them for genetic experiments.
An alien probe unleashes a devastating virus on Earth, threatening to kill both the human and Taelon races.
The Resistance races against time to infiltrate a remote Taelon lab to destroy the alien probe that holds the Liberation movement's secrets. Vint Cerf, "Father of the Internet", makes a special guest star appearance.
A renegade alien appears on Earth to exact revenge on the Taelons.