The Xindi are not a single species, but six, that all evolved from different genetic stock on the planet Xindus in the former Delphic Expanse. Under the influence of the Sphere Builders, the Xindi became embroiled in the Temporal Cold War, and launched a devastating attack on Earth in 2153, attempting to eradicate the human species. Their plans for a final assault on Earth were disrupted by Enterprise, and peace was eventually established. The actions of the Xindi inadvertently set in motion the chain of events that led to the United Earth's emergence as a major interstellar power, and the subsequent founding of the United Federation of Planets. (ENT: "The Expanse", "The Xindi", "Zero Hour", "Storm Front", et. al)
- In at least one possible future timeline, the Xindi became members of the Federation by the 26th century. (ENT: "Azati Prime")
The six Xindi species eventually created a united civilization, though one species, the Avians, were believed to have gone extinct before the 22nd century. The remaining five species were governed by Xindi Council, consisting of two representatives from each species.
Despite the apparent physical differences, the Xindi species are extremely similar on a genetic level, sharing over 99.5% of their DNA. From the physical standpoint, all six species shared distinctive ridges on their cheekbones and foreheads. (ENT: "The Xindi")
During the Great Diaspora in the 2030s, the different Xindi species engaged in a civil war that ended with the destruction of their homeworld, with only ship-board Xindi surviving. Thanks to the Sphere Builders, whom the Xindi called ‘‘"The Guardians"’’ whom they came to view as god-like beings, they were able to find habitable worlds.
In the 2140s, the Guardians warned the Xindi Council that unless they destroyed Earth, the Humans there would destroy their future homeworld. The Aquatics were originally against the building of a Xindi superweapon; however, they changed their minds after the Guardians presented a visual record of their future world's destruction. They eventually agreed to create it and were assigned to build the Xindi weapon, because they were the most level-headed and efficient. The weapon was built underwater on Azati Prime.
In late 2153, they agreed to the launch of a miniature prototype Xindi superweapon, which killed seven million people on Earth. This led to the Humans sending Enterprise into the Expanse to stop the weapon. Throughout the following year, the Council monitored their advancement, as the Reptilians and Insectoids suggested alternate ways of exterminating the Humans. At the Council meetings, the Aquatic councillors were often the more balanced and level-minded members, suggesting that they continue monitoring them instead of sending a fleet to destroy them right away.
In 2153, after finding the location of the weapon, Captain Jonathan Archer, of the Earth ship Enterprise tried to use the Insectoid shuttle to get into the weapon and destroy it, but was captured before he could do so. While he was away, the Xindi-Reptilians and Insectoids opened fire on Enterprise, nearly destroying it.
Degra didn't trust Captain Archer, but couldn't let go the possibility that he was telling the truth. In early 2154, after the Xindi Council ordered the Reptilians to cease their attack on Enterprise, Degra had the Aquatics, the only ones he could trust, transport Archer back to Enterprise. After he briefly regained consciousness aboard their vessel, he was put in an escape pod and left adrift for Enterprise to find.
The Aquatics finally decided to help the Humans when Enterprise promised to destroy the Sphere network. They sent several of their ships to fight the Reptilians and the Insectoids with Enterprise, the Arboreals and the Primates.
Unfortunately, most of their fleet was defeated when the Sphere Builders triggered the spheres to create massive anomalies, which breached the hulls of the Aquatic ships, releasing water into space.
In the Star Trek: Prometheus continuity after locating and settling on the third planet in system SNC 461206 in Sector 441 system with the assistance of the Federation and establishing it as their new homeworld. The planet, known in Federation databases prior to the colonization as SNC 461206-III, was renamed New Xindus by the Xindi Council who had been granted a special dispensation by the President of the Federation to officially change the name of the planet. Following the establishment of Xindi-Aquatic, Xindi-Arboral, Xindi-Primate, Xindi-Insectoid, and Xindi-Reptilian settlements on the planet The Xindi Council petitioned the United Federation of Planets for membership, on behalf of their new homeworld and their colonies in the late Twenty-third century following a protracted period of peaceful diplomatic contact.
In the Star Trek: Prometheus continuity the actions of the Sphere Builders and the actions of the crew of the Enterprise in the twenty second century brought about the Xindi's entry into the Federation in the early twenty-fourth century.
In the early 2330's a single colony of the long thought extinct Xindi-Avains was discovered on an isolated planetoid in the Delphic Expanse. Following the re-establishment of contact with their Xindi cousins in the Federation the Avians petitioned the Federation for membership, which was granted, and re-located their colony to New Xindus.
During the Federation Civil War , the Xindi homeworld of New Xindus was the site of a major conflict based almost completely on the ground. After the end of the War, New Xindus was declaired a Safe Zone, where no faction could build a base, the Xindi remained part of the Federation however.
In the Battle of the Sol System, a Xindi-Arboreal named Sodar was the captain of the USS Nightingale, and made the plea before the Klingon High Council for their support.
Until the mid-22nd century at least, the Xindi nearly worshiped the Guardians, thinking of them as saviors. Xindi children were taught to revere and give thanks to them each night. It was considered a grave offense to doubt or question a Guardian. (ENT: "The Council")