The Colonists are an extraterrestrial species and are also the primary group of antagonists in the science fiction television show The X-Files as well as the first X-Files feature film. The mystery revolving around their identity and purpose is slowly revealed across the course of the series. In the series' plot, the Colonists are collaborating with a group of United States government officials known as the Syndicate in a plan to colonize the Earth, hence their name.

According to the series mythology, an extraterrestrial lifeform, known in the series' mythology simply as the Colonists, were originally present on Earth in the early stages of human evolution. They highly resemble the well-known "grey aliens" in their mature form. In their immature stage, they are more yellowish-colored, tall, and very aggressive, possessing fangs, claws and scale-like texture of their skin. This immature form is a protective stage, able to viciously defend itself from birth. This outer skin is eventually shed when the alien develops into its mature form. The immature form resembles that of a reptilian extraterrestrial and is referred to as the "long-clawed" form.

The aliens were forced to abandon the planet during the last ice age as their viral form is deactivated by extreme cold. Upon their departure, they left behind underground deposits of the black oil virus, in preparation for their return. The virus apparently contains the aliens' genetic blueprints, awaiting reconstitution when the master species returns to Earth. While away from Earth, the Colonists evidently sought out life throughout the universe in an effort to subdue other species and take over the universe. Purportedly, the Colonists planned on returning to Earth in the year 2012, as The Smoking Man (William B. Davis) later remarks to Fox Mulder (David Duchovny) that the ancient Mayans were so terrified that they stopped their calendar on the exact date of colonization: December 22, 2012. The Colonists eventually returned to Earth in 1947 when one of their ships crashed in New Mexico due to exposure to magnetite in the surrounding rocks. Shortly after this event, a select few power brokers, mainly in the United States and the Soviet Union (though some also came from other nations), first learned of the Colonist plot to retake the planet. These men eventually formed the Syndicate; they included the Well-Manicured Man (John Neville), The Smoking Man, and Bill Mulder (Peter Donat), among others.

The Syndicate threatened to use nuclear weapons to render the Earth uninhabitable to the Colonists due to extreme cold. As such, humanity was spared immediate invasion, and The Syndicate began negotiations with the Colonists. In 1973, an alliance was created and an agreement was reached that a small group of humans would be allowed by the Colonists to survive by becoming alien-human hybrids. The date for recolonization was firmly established in 2012 so that both sides could work on creating an alien-human hybrid before the arrival of the Colonist fleet. These hybrids, if successful, would serve as a slave race for the Colonists – the Syndicate and other chosen humans would receive the hybrid genes and be spared. In exchange for the Syndicate's cooperation, the Colonists handed over alien embryos as a source of genetic material for the hybrid experiments, as well as allowing limited military use of their technology and resources (such as the Alien Bounty Hunters), and promising that the heirs of the Syndicate members, who were turned over to the Colonists as an act of good faith, would survive the takeover. Meanwhile, both sides had a secret. The human conspirators would attempt to develop a vaccine for the alien virus in an effort to save all of humanity. The Colonists pretended that mass infection of humanity by the black oil would make them a controlled slave race, but in reality the oil would give birth to new alien beings within the human hosts resulting in re-population rather than colonization.

The Bounty Hunters are a distinct group from the Colonist aliens. Although all Colonist aliens are shape-shifters, the Alien Bounty Hunters readily take the shape of humans and are tasked with policing their plans and tracking down and eliminating any threats. The bounty hunters have green blood that contains a retrovirus which, when exposed to humans, is lethal. The alien blood can burn through most surfaces like an acid, and can kill a normal human if exposed for too long to its noxious fumes. In addition, the alien's blood causes human blood to coagulate into a jelly-like substance, but its effects can be neutralized by extreme cold. The Bounty Hunters, and any member of the Colonists' race, could also only be killed by piercing a small area at the base of the neck; the bounty hunters carried a kind of alien stiletto-like weapon to assassinate rogue aliens and to destroy imperfect alien-human hybrids. Once dead, their bodies would rapidly dissolve into a pool of their severely acidic blood, which would eventually evaporate.

Inconsistent with this arc, in season 8 episode 2 "Without" Scully kills the bounty hunter by shooting him with her gun. He oozes green blood, yet neither she, nor the other FBI agents who enter the room while the body is disintegrating, are affected by the green acid-like blood.

The Alien Rebels, those aliens that opposed the plans of the alien Colonists, are of the same species. The distinguishing characteristic of the Rebels is that they have had all of their facial orifices sealed shut in an effort to avoid absorption of and subsequent infection by the parasitic black oil; this led to a somewhat grotesque appearance. In the latter seasons of The X-Files, the role of the Bounty Hunters on Earth has largely been taken over by the Super Soldiers, human replacements capable of withstanding incredible amounts of damage.

In the two-part episodes "Colony" and "End Game", Chris Carter and Frank Spotnitz along with some help from David Duchovny created what would become a recurring character named the Alien Bounty Hunter. According to Carter, Duchovny came to him and said "wouldn't it be great if we had like an alien bounty hunter?" Carter was positive towards the idea and acted upon it. The actor Brian Thompson auditioned for the role in a casting session, where he was competing with another actor. Spotnitz and Carter did not have much time to cast this character, but they knew this casting would be important since they intended the character to become a recurring character. Thompson was chosen according to Spotnitz because he had a very "distinctive look" about him, most notably his face and mouth. After casting him, they told Thompson's agent that he needed a hair cut, because he was originally envisioned as a U.S. Air Force pilot who'd been shot down. When Thompson came to Vancouver, British Columbia, Canada there had been some "misunderstanding" between them, and he had not been told of the hair cut. So the hairstyle seen in this and every episode since was a "compromise" between Thompson and the producers.