The Q Civil War was a conflict between two factions of the Q Continuum that took place in 2373. Fought between those who believed in the teachings of Quinn, called the Freedom Faction, and the forces of the status quo, the deeper nuances of the conflict were beyond the understanding of "mere" Humans.
Q attempted to represent the war to Humans through the format of the American Civil War, with the followers of Quinn as the Union and the status quo as the Confederacy.
Origins and war
The suicide of Quinn in 2372, the first death of a Q in many years, caused chaos and upheaval in the Continuum. This was because even though he was gone, his calls for freedom and individualism continued to echo in the ears of those who believed in his teachings. One among them, Q (who had until recently been a support of the status quo) claimed to have "sounded the trumpet and carried the banner". He was considered the ringleader. Naturally, others followed. The status quo tried to crush the Freedom Faction, but they fought back.
A cosmic struggle for supremacy ensued, battle spreading quickly and causing hazardous repercussions throughout the Milky Way Galaxy. These included anomalous supernovae, caused by spatial disruptions within the Continuum and creating a negative density false vacuum that sucked surrounding matter into the Continuum. They were described by Q as "galactic cross fire".
As represented through the civil war lens, the war contained battles, multiple encampments, and enemy patrols. Cannonballs and lead charges were fired, which represented more advanced weapons capable of wounding Q's even despite their immortality. Wounded Combatants were seen bleeding or even sporting amputated legs. Looking at the aftermath of a battle through her civil war perspective, Captain Kathryn Janeway opined that the followers of Quinn were not on the winning side.
Seeking to bring an end to the conflict, Q proposed conceiving a child with Kathryn Janeway, whom he had met the previous year. Q hoped that a Q/Human hybrid child would unite the best qualities of both species, "an infusion of fresh blood, a new sensibility, a new leader, a new messiah".
However, Janeway refused to accept Q's plan, arguing that, aside from the fact she did not want to mate with him, his plan, though noble, offered only a "quick fix" without addressing the underlying problems that the conflict was about. She instead proposed he mate with Q.
Janeway then attempted to negotiate a cease fire to end the civil war by contacting a leader of the opposition faction, Colonel Q. The status quo agreed that the war needed to end soon, lest irreparable damage to subspace occur, but believed the most expedient way was to executing Q. Janeway was to be executed too, for "collaborating with the enemy."
Q then made his proposal of conceiving a child to his old girlfriend, and she accepted. The two touched fingers, and in a small glow of energy created the first new Q in over ten millennia. This newborn child (nicknamed Junior) was hoped to be a herald of a whole new era of peace for the Continuum, and brought about a quick end to the civil war. In gratitude for her assistance, Q named Janeway the "godmother" of his new son. (VOY: "The Q and the Grey")