The Jedi set up camp in and around a facility was once controlled by the Galactic Empire during their occupation of the moon. After the defeat of the Empire, the base lay abandoned for many years. The Order's StealthXs were stored under camouflage netting in burn zones from where the debris from the Death Star II rained down. A scouting team went into nearby caves and began the process of converting them into training facilities. The cavern system would also help defend against orbital sensors. C-3PO was brought by the Jedi in order to please neighboring Ewok tribes.
Queen Mother Tenel Ka Djo of the Hapes Consortium traveled to Endor shortly after Caedus kidnapped her daughter Allana, and met with Grand Master Skywalker who informed Tenel Ka that the Jedi Order would help rescue her daughter from the Anakin Solo.
General Tycho Celchu later traveled to Endor with Captain Syal Antilles to relay an official request from the Galactic Alliance government to the Jedi Coalition to return to the service of the Galactic Alliance. Even though it was believed that the request was from Admiral Cha Niathal, or at the least factions of the Galactic Alliance loyal to her, Skywalker refused the offer as it could've left the order at the mercy of Darth Caedus. Realizing General Celchu would report the location of the Jedi base to his superiors and that Darth Caedus would sooner or later learn where the Jedi were hiding, Luke decided that the Jedi would leave Endor before Caedus could act against the Jedi.
Before the Jedi abandoned their base on Endor for the Transitory Mists, Ben Skywalker met with his aunt, uncle, cousin, and father to talk over his conviction that Alema Rar had not been responsible for his mother's death and to provide a secret holorecording of Darth Caedus's confession.
The base was soon discovered by Tahiri Veila, Caedus' new Sith apprentice, but, by that point, the Jedi had already left for Shedu Maad.