The Freedom was first launched under the command of Commodore Jeff Pelletier. He commanded it through her first year in space, before being recalled to Starfleet, at which point the first officer Marko (Mark Anderson) took command through her mission and subsequesent return to base. Captain Merritt then too took command temporarily for several missions. During Merritt's last mission in command, the serial killer Kalendra infultrated the ship and killed a half-dozen personnel, including two officers. Merritt was charged with violations of several Starfleet codes during that mission, but committed suicide by stealing a shuttle and crashing it into StarBase 118 before she could be brought to court marshal.
Starfleet appointed a new commanding officer for the Freedom soon after: Commander, (and soon after Captain) Sandolphan Aquiss. He commanded the Freedom for her next few missions, including a mission where she attacked a damaged Borg Cube. During that mission, Aquiss and deck officer Lieutenant Commander Robert Falcon were assimilated by the Borg Collective, but were rescued by the ship's counsilor, Adler Wong. The Freedom was later involved in a mock battle against the Sovereign-class U.S.S. Ithaca in a test of a new shielding technology, the Wall of Light. It protected a ship by moving it slightly into another dimension, making a bubble of brightly colored energy where the ship had been. The downside was it turned the ship essentially into a turtle, unable to move or fire weapons, but protected from anything. During the test, Aquiss became possessed by a number of psionic beings, forcing him to beam most of the personnel off of the Freedom. He was able to force the beings to leave him and evacuate the last remaining people from the Freedom, but was forced to abandon the Freedom into another dimension by locking the shield on. That would have been the end for a ship of lesser stature and history than the Freedom. Later, Aquiss himself was lost to the same dimension, and both he and the Freedom were recovered by the crew of the Ithaca. The Freedom was placed in storage at StarBase 118, where she was recovered by former crewmember Captain Torack Demma, and taken to Deep Space 72 for repairs and refitting. After a short stint under the command of Commander Falcon, she was returned to StarBase 118 for a full overhaul of her computer and engine systems to fix numerous old-age problems.
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