Set 500 years in the future, Humans have colonized and terraformed a planetary system of unknown location. The system contains core planets and "border" planets. As a general rule, the farther out one travels, the less civilized society becomes. The core planets allied under a single government (The Alliance) and declared war upon those planets that wished to maintain their independence ("The Browncoats"). This series of events is recalled as the Unification War. The Alliance was victorious, and those surviving independents migrated towards the outer planets.

Relatively little is known of the actual war itself (for example, we do not yet know who fired first). One of the bloodiest battles of the war was the Battle of Sturges, which was fought over a hoard of money. The Battle of Sturges never made it to the ground so they remain floating in space. It is never stated where the remains of the battle are but they are but they are known to the crew. Other conflicts mentioned in the series are the Battle of Du-Khang in 2510 (featured in "The Message") and a long winter campaign in New Kashmir. The last and most grisly major battle in the war was the Battle of Serenity Valley, in which Malcolm Reynolds and Zoë Alleyne fought for The Independent Faction.

The Battle of Serenity Valley is considered the final decisive battle in the Unification War. The battle that began in May 2511, while not the final battle of the war, was certainly the end of the line for the Independents, who had sixteen brigades and twenty air-tank squads in position. Taking place on Planet Hera, the battle lasted seven weeks before Independent High Command officially surrendered to Alliance forces. The Alliance won because of superior numbers and a brilliant deep-flank strategy by General Richard Wilkins (a reference to the TV series Buffy the Vampire Slayer). Overall troop casualty rate was 68%. A deleted scene from the movie Serenity claims the Independents' command actually surrendered after five weeks of combat, but the soldiers fought on for an additional two before finally giving up.

Malcolm Reynolds, of the 57th Overlanders, was a sergeant, but by the end of the battle, so many officers had died that he commanded over 5,000 troops. Reynolds and what was left of the army held the Alliance at bay. To their dismay, orders came to lay down arms and surrender. What Mal hoped to be the sound of the Independent air support was in fact that of the Alliance cruisers landing. Even though the shooting stopped, the battle was not over. For a week, while the Alliance and Independents sorted out the surrender, Browncoat and Purplebelly alike were left hungry, bloody and dying on field of battle. By the time rescue ships arrived, there were about 150 left of the 5,000 Mal led. He and Corporal Zoë Alleyne were the only two survivors of their original unit, known as the Balls and Bayonetes Brigade.

Malcolm Reynolds' ship, of which Zoë is second in command, is a Firefly-class transport ship, named Serenity after this particular battle; the rubric "no one leaves Serenity, you just learn to live there" being a bittersweet reference less to the ship's status as a home as to the catastrophic body count at the battle. The Battle of Serenity Valley is a sensitive issue for both Mal and Zoë, and crew member Jayne Cobb often gets into trouble with the two by bringing up the battle's grim characteristics in an attempt to push Mal.