By taking control of one of sixteen species, players attempt to claim dominance in the Orion Sector.
It turns out that what was thought to be Antares in Master of Orion II was really "ConJenn", a forward base for the Antarans. After faking their eradication for 25 Galactic Cycles, the Antarans returned to defeat the young races of the Orion Sector over the course of another 25 G.C. They enslaved whole planets, destroyed all technologies and military outposts and effectively made it impossible for a retaliation of any kind.
At the beginning of MOO3, set a thousand years later, the Antarans have mysteriously disappeared. The disappearance coincides, it is discovered, with the release of a prototype virus-like organism, Harvester Gamma. Harvester Gamma would infect and multiply, potentially destroying any species it was set loose on. In an ironic turn of events, the organism was accidentally loosed on the Antarans, wiping out 98% of their population in the Antaran sector.
The survivors on Orion declare themselves the "New Orions" (not to be confused for the "Ancient Orions"). The remaining Antarans, in a remote outpost, begin work on another Biological weapon, called Harvester Zeta while the "New Orions" grant the rebellious colonies in the Orion sector a new Orion Senate, and pretend to play the role of benevolent, and enlightened leadership. The Antarans unleash the Harvester Zeta on a remote Human settlement, but Harvester Zeta, a sentient organism, begins to call itself the Ithkul and form its own colonies like the other races in the Orion Sector.
The gameplay in Master of Orion 3 differs from Master of Orion I and II. This is somewhat due to a change of development staff, as well as the implementation and removal of various features. The new features of 3 were derived from a fan vote, whereby the features of the game would be dropped or minimized or maximized according to what players wanted. However, many of the ideas that were voted for were not taken aboard by the developers (such as colonization of moons and asteroids, and a racial ethos system).
New to the series is ground combat, which allows units to wage war in a real-time "paper, scissors, rock" battle system. As well as this, one large change in MoO3 from MoO2 is that micromanagement is toned down significantly.
Upon choosing a species and race, players undertake the conquest of the Orion Sector through either diplomacy, military conquest, or technology.
- Leadership of the Galaxy - Winning election to the Galactic Senate. In order to do this, players are required to get elected by the other races in the galaxy. This may or may not require military force, but always requires cold, hard diplomacy.
- Military Conquest - Destruction of all other races.
- Finding the Antarian Xs - As a departure from the series, instead of just conquering the Antarian homeworld (though players can conquer the Orions), players can find the Antarian Xs, which reveal more of the Antarian's backstory. Doing this requires sending out high-priced exploration fleets.