The Imperial-class Star Destroyer known as Whirlwind functioned as the flagship for Admiral Blitzer Harrsk's Arrowhead Command within the Imperial forces, up until the Battle of Endor. After the demise of Palpatine's clones some years later, this Star Destroyer was one of a dozen under the control of Harrsk, who had risen to the rank of Supreme Warlord.
During the war waged by the Galactic Empire against the Alliance to Restore the Republic, the Whirlwind operated as the command ship for Admiral Harrsk's forces in the area known as Arrowhead. This region marked the junction of galactic regions including the Slice and the Core Worlds. At the Battle of Endor, Arrowhead Command was attached to the Imperial Navy's Death Squadron. During the battle, the Whirlwind took damage, resulting in an internal explosion that killed its captain, Bolla Thoath. Shrapnel from the explosion also struck Harrsk, causing brain damage and disfiguring his face. Although the battle was intended as a trap for the Alliance, the Rebels achieved victory at Endor, forcing the Imperial forces to retreat. Harrsk initially followed the retreat order after surviving, but his injuries had driven him mad. He subsequently broke away from the Empire, fleeing to the dangerous Deep Core region of the galaxy and establishing the renegade Zero Command faction.
Eight years after the events of the Battle of Endor, Harrsk's forces were engaged by a fleet of Victory-class Star Destroyers led by High Admiral Treuten Teradoc, a rival warlord. In this conflict, Harrsk lost his flagship, the extensively modified Star Destroyer known as the Shockwave.
Driven by a desire for vengeance, Harrsk assumed command of his fleet from the bridge of the Whirlwind. With assistance from Admiral Daala, who directed operations from the Star Destroyer Firestorm, he launched a counterattack against Teradoc. During this raid, Daala, frustrated by the disorganized state of the Empire and the loss of her trusted second-in-command, Commander Kratas, used ion cannon fire to disable the Whirlwind. She then opened a comm channel to both Harrsk's and Teradoc's forces, demanding they cease their internal conflicts and select a commander to unite the remaining Imperial forces against the New Republic. Daala threatened to self-destruct the Firestorm, destroying both the Whirlwind and all other nearby ships, if her demands were not met.
The Whirlwind was absorbed into Daala and Pellaeon's United Warlord Fleets.
Following the Tsoss Beacon negotiations and the re-establishment of unity among the Deep Core warlords, the Whirlwind was integrated into the united fleet under the command of Daala and then-Vice Admiral Gilad Pellaeon. It became part of a force consisting of forty-five Star Destroyers under Pellaeon's leadership, and was also included in his personal fleet of thirteen vessels.