Near the end of the war, Colonel Q attacked and surrounded the manor that Q and Janeway were in, where he requested Q's surrender. Q refused and both he and Janeway were able to escape.
Janeway later entered Colonel Q's encampment and requested a cease fire on Q's behalf, stating that Q had a resolution for ending the war. Colonel Q admired her bravery for entering the camp unescorted and unarmed, but ultimately told her that Q was to be executed. He subsequently arrested Janeway for "collaborating with the enemy," which he also stated was a crime punishable by death.
The following day, as Colonel Q prepared the firing squad, members of the opposing forces, which included members of the USS Voyager crew wielding Q weapons, attacked his encampment, and the Colonel was eventually captured by Tom Paris.