In the 2240s, MacDougan served as an instructor at Earthforce Academy. As part of their training, MacDougan would pose moral conflicts for his students, among them a cadet by the name of John Sheridan. He told them that soldiers are not machines and must think for themselves to decide if an order is moral or not. MacDougan would also go on to teach one Cadet Leo Frank.
In 2261 he and his ship were assigned to the illegal blockade of Proxima III ordered by President Morgan Clark. He went to great lengths to avoid attacking civilian targets while stationed there. During the Battle of Proxima III, MacDougan broke radio silence and opened communications with the rebel commander, Captain John Sheridan. Following this conversation, during which Sheridan reminded his former teacher and old friend of his lessons on morality, MacDougan refused to engage the Whitestar fleet, feeling that it would be an action in support of illegal orders.
As a result, Captain Trevor Hall promoted Commander Robert Philby and ordered him to take command of the Vesta. He proceeded to bring the Vesta into the fight, but only for a short time. The crew of the Vesta mutinied against Philby and quickly returned command to MacDougan. He ordered the Vesta to stand down, and declared his ship non-hostile to the Whitestar fleet. Later he would join up with Sheridan's forces and participate in the latter battles of the war.
After his defection, Clark loyalists in Earthforce briefed all starship captains that MacDougan and his crew had been executed and that a Minbari crew had been put in charge of the Vesta. His voice was enough to convince Captain Leo Frank of the EAS Cadmus to stand down.