A race of super-intelligent and highly advanced, androgynous people known as the Taelon travel to 21st century Earth and appear to be completely benevolent. They bring the solutions to many of humankind's problems and freely share them. After three years, they are well intergrated into every part of Human life. But despite their apparent friendliness and good-will, a group of people, led by multimillionaire Jonathan Doors, are not convinced that the Taelons have only Earth's best interests at heart. The Taelon call themselves Earth's "Companions", and spread out across the planet. Each Companion reports to the Taelon Synod, and has Humans who serve as guards and liasons. This latter group have cyber viral implants in their brains, that redirects Human motivations towards Taelon interests.

Like every Roddenberry creation, EFC enphasises the ambiguity of contact between humans and aliens, especially aliens who are greatly advanced. The Taelon have an agenda that they will stop at nothing to achieve. However, the appearance of a second, third and then a fourth race complicates matters even further. The main focus of the storyline is on the Taelon Companion to North America, Da'an, and "his" Human implants, ex-special forces, ex police officer William Boone, and FBI agent Ronald Sandoval. Boone and his partner, ex-marine Captain Lili Marquette, who works as Da'an's pilot, are also secretly working for the liberation movement. However, after Boon's death, he is replaced by Liam Kincaid, a part-Kimera Human.