The New Republic forces had joined with the Hapan fleet to destroy the Stellar Imperium once and for all. The Angwel Collective was a small group of planets that had been subjugated by the Stellar Imperium many years earlier, but left nominally independent as a front for Sith activities. Empress Shira put her own agent, Darth Inferna, as the Senator from the Collective, and they worked hard to stall progress in the New Republic Senate and make it difficult to organize the military against the Imperium.
Initially, the Hapans and the Imperial Remnant, what had not fallen into Stellar Imperial control, remained independent. By 25 ABY, the Imperial Remnant had a very loose alliance with the Stellar Imperium, mostly a "leave us alone and we'll leave you alone" agreement, plus some modest trade benefits. The Hapans did not enter the conflict until early 29 ABY, to ally with the New Republic.
The Angwel system was a good place for Shira to hide her fleet and build it back up, but her fleet was still too scattered to withstand the pounding given by the combined Hapan and New Republic fleets. Angwel was no longer part of the New Republic, because Darth Inferna had been exposed as a Sith and a traitor - and, in fact, by the time of the Battle of Angwel, she was dead.
Shira refused to surrender, and when Jaina Solo and Zekk went to capture her, she fought them. They had no choice but to kill her. At the time of the battle, Jaina and Zekk were the most advanced Jedi available for the mission, because the Cyalax Virus had stripped almost everyone else of their Force powers.
Admiral Hocke was the next-in-command of the Stellar Imperial fleet after Shira's death, since Darth Inferna had died and Lord Welk had disappeared. He immediately signed a peace treaty that ceded most of the Stellar Imperium to the Imperial Remnant, and the war was over.