"Establishing immediately that the canonical ending involves Blair destroying the K'tithrak Mang, the newly-promoted Colonel Blair, along with Col. Ralgha "Hobbes" nar Hhallas, is scheduled for a transfer to the "Special Operations" division of Intelligence, under Col. Taggart, who is Chief Field Officer of Intelligence and Special Operations in the Enigma Sector. Their transfers are delayed, however, by increasing Kilrathi presence in the Pembroke System, including the brand-new Gothri-class heavy fighter; even worse, the Rigel Supply Depot is attacked. ...By Confederation ships, which open fire on Blair when he arrives to investigate."
Source: Wikipedia, "Wing_Commander_2," available under the CC-BY-SA License.