The game takes place on the titular space cruiser, in which a small band of outcasts hides away in a tiny corner of the ship. Harbinger is a slave ship, and most of its occupants are trapped aboard under the iron-fisted control of a being known only as "the overlord." Amidst the backdrop of a major war between the ship's primary factions, you and your band of misfits attempt to stay alive.

There are only three character classes to choose from in Harbinger: human, gladiator, and culibine. The gladiator is a cyborglike robot infused with the consciousness of a living being, while the culibine resembles Diablo's sorcerer character, though in practice, all the classes play about the same. While the different classes have special gadgets they can use--the gladiator can control remotely operated cameras and the human can drop mines of varying types, for example--these items actually don't figure prominently into the gameplay because of play-balance issues between the attack types.