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The Lakota went on to coordinate Starfleet Security forces planetside during Admiral James Leyton's attempted coup d'état, with Leyton declaring martial law. During this time, the Lakota's phasers were upgraded and the ship received a supply of quantum torpedoes. (DS9: "Homefont")
Under the command of new Captain Erika Benteen, the Lakota intercepted the USS Defiant in an attempt to quell Sisko's anti-coup attempt. The battle between the two ships was muted, as both ships were reluctant to do more than disable the other. As a result, Leyton revised his orders; the Lakota must destroy the Defiant. Benteen refused, standing the Lakota down and allowing Defiant to proceed to Earth. (DS9: "Paradise Lost")
In the aftermath of the war, the Lakota sat in an out-of-the-way drydock for several years, with Starfleet unwilling to assign a new crew to the ship. It wasn't until 2378 that the Lakota was recommissioned to participate in Project Restoration. Under the command of Captain Tiris Jast, the Lakota's involvement in reconstructing a new Deep Space 9 was seen as a symbol of the Federation's resolve to put the past behind them. Another part of that symbolism involved the assignment of Lt. Commander Tom Paris as Lakota's first officer. As an officer who had not lived through the civil war, Paris presented a unique perspective among the crew. (PDN: "Restoration")