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For information relating to the Federation Civil War in the Pendragon reality in Star Trek fanon, see Federation Civil War (PDN).

In the Pendragon reality, the Federation Civil War was a civil war between factions within the Federation and Starfleet. The war started after Vice Admiral James Leyton successfully led a coup d'état.

A significant battle during the Federation Civil War was the Battle of Deep Space 9 in 2372. During the battle, USS Aotearoa commanding officer Captain Liam de Gaillimhe ordered his crew to destroy escape pods jettisoned from Deep Space 9 in case one or more contained a Founder. Captain Daniel Radke and his crew moved the USS Cuxhaven to protect the escape pods. Radke and his crew won the upper hand, "beating the living daylights" out of de Gaillimhe and his crew, according to Noah Wrightson. Radke supposedly told de Gaillimhe to, "stop giving into his lust for blood." (Star Trek: Pendragon: Other Knights anthology: "Gravity")

After the war ended, Project Restoration brought a new Deep Space 9-II online in 2379, 5 years after the war ended. (Star Trek: Pendragon: Other Knights anthology: "Gravity")

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