Gene Roddenberry's Earth: Final Conflict is set in the near future, after the arrival on Earth of an advanced species of aliens called Taelons, or Companions. From the outset, they professed supremely benevolent intentions and used their superior technology to help Earth solve many of its most pressing problems. Though regarded as saviors by the general public, the Taelons inspired the profound distrust of enigmatic billionaire, Jonathan Doors (David Hemblen), who founded an underground resistance movement to expose their hidden agenda.

While capitalizing on the devotion of the masses, the Taelons secretly began trying to harness Earth's human resources. In hidden labs, they conducted frightening bioengineering experiments on kidnapped human subjects. As the series progressed, the Taelons themselves came under attack. One of their leaders was killed by a probe unleashed by the Jaridians, a race of warrior-like aliens bent on destroying them. The incident prompted Da'an (Leni Parker), the Companion leader assigned to the United States, to appoint Major Liam Kincaid (Robert Leeshock) as his new protector.

Kincaid, a human/Kimerian hybrid with unique mental and physical powers, took up the secret mission of his murdered predecessor to discover the Taelons' real motives. While serving Da'an, he spearheaded covert operations for the Resistance, eventually stepping in as its leader when Jonathan Doors made a bid for the White House against Taelon sympathizer President Thompson. Doors ultimately lost the election after Thompson was wounded in an assassination attempt blamed on the Resistance.