In the early 21st century, the different Xindi races fought for control of the Xindi Homeworld. During this long war, the Xindi-Avian race was eradicated. In the end the Xindi-Reptilians and the Xindi-Insectoids forged an alliance which resulted in the destruction of the planet, sometime around 2023. This began the era known to the Xindi as the Great Diaspora, as the various Xindi species that survived the destruction declared peace, and sought to work together to find and establish a new homeworld. The Sphere Builders, known to the Xindi as The Gaurdians, led them to habital planets.
In 2153, the Xindi became involved in the Temporal Cold War (due to the involvement of the Sphere Builders) and were led to believe that they would be destroyed by the human race around 2653. Their reaction was a project to build a weapon that would destroy Earth and wipe out humanity before this event could take place. A test probe sent midway through that year killed 7 Million humans and devastated a large stretch of Earth's surface, from Florida to South America. Earth responded with sending their flagship, Enterprise, into the Delphic Expanse in order to destroy the probe.
According to Daniels, the Xindi were intended to join the Federation, and prove to be of valuable use in the war against the Sphere Builders. By the 26th century, Xindi are serving aboard Starfleet vessels, including the Enterprise-J.