The Eta-class shuttle saw used mid way through the first year of the war as part of a Republic force to free Jedi Master Eeth Koth. The shuttle was piloted by Anakin Skywalker and Adi Gallia to board General Grievous's Separatist Destroyer while Obi-Wan Kenobi and the rest of the fleet provided a distraction for the Separatist ships. Skywalker used the tactic of bringing the shuttle out of hyperspace right in front of the destroyer to board discretely. Once Koth had been rescued, Skywalker returned to the ship with his troops to depart from the destroyer while Gallia went to assist Kenobi in his effort to capture Grievous. However, Kenobi's transport was destroyed, so the shuttle was used to bring Kenobi, Koth and the rest back to the fleet.
The ship saw further use that year, once again, by Obi-Wan, Anakin and Jedi Padawan Ahsoka Tano to travel to the Chrelythiumn system in response to a two thousand-year-old Jedi distress call that was sent by the Father, a powerful being known as a Force Wielder who resided on Mortis, to see for himself the Chosen One. Upon arrival, the Jedi's shuttle, lost all functions, went off any outside scanners and was pulled into the monolith. When the three resumed consciousness, they found the ship was almost completely inactive and had landed on the planet. They were soon met by another Force wielder, the Daughter, who took them to meet the Father. But herself, with Anakin, was separated from Kenobi and Tano by a trap set by the third being of the planet, the Son. When the Daughter departed from Anakin, he told his companions to return to the shuttle and send a distress call. When they returned to their landing site, they found the ship had vanished and the Son was in its place. The next day, after Anakin proved himself to the Father, the latter offered to him the opportunity to rule the planet and his children when he died. But when Anakin refused, he and the other Jedi found their shuttle at the Father's monastery and departed Mortis. Unfortunately, they were forced to remain on the planet with the Son kidnapped Ahsoka to turn her to the Dark side, and when Skywalker pursued, their shuttle crashed on the surface. Later, after she was rescued, Tano was tasked with making repairs to the shuttle while Kenobi and Skywalker then traveled to find the Son on jumpspeeders that were stored aboard the ship. Soon following, just after she had made adequate repairs, Obi-Wan contacted her informing her that Anakin had joined with the Son and she had to disable the shuttle to prevent them from leaving the planet. Ahsoka reluctantly obeyed, severing at least two key components from the ship, and traveled off to rescue Kenobi. The world of Mortis soon came to and end when the Father returned Anakin to the Light side of the Force and he was forced to kill himself, thereby severing his Son's power and, before his death, assuring Skywalker he would bring balance to the Force, as the prophecy of the Chosen One foretold. Then, with his death, the world was unable to sustain itself and the Jedi trio was somehow transported back to space aboard their shuttle.
Later on, the Eta-class shuttle was used by Kenobi to travel to the world of Raydonia to confront the recently resurrected Sith lord, Darth Maul. Sometime afterward, a variation of the Eta shuttle was used by Palpatine to travel to Mandalore.
- Grievous Intrigue (First appearance)
- The Academy
- Assassin (Appears in flashback(s))
- Hunt for Ziro
- Altar of Mortis
- Ghosts of Mortis
- The Lawless
- The Unknown