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Marathon: Invasion will include numerous changes to the basic Ares engine. Three basic changes will apply to the entire game:
-There are 6 races replacing the basic Ares races, each with rewritten ship classes and concepts. The basic classes are referred to as "fighters," "corvettes," "destroyers," "battleships," "dreadnoughts," "assault carriers," and "colony ships," each taken from the Marathon series. The first five are fighting ships, specialized in destroying the ships slightly smaller than it. Assault Carriers carry large numbers of Elite and Troopers, as well as carrying fighters. Colony ships are used as described below.

-There are two types of planets. Colonized, and uncolonized. Players will almost universally begin with a colonized planet, as will the enemy. Usually, the other planets in the system will initially be uncolonized. Players must move a colony ship there to activate its resource production and ship-building abilities. Colonies can be removed from planets by the use of a particular weapon, a different weapon for each race.

-Each ship carries a number of "elite" and "troopers" which can be teleported onto a ship. After a certain point, the ship will be captured, but in any event, the ship can take large amounts of damage. Elite (such as the Marine from the series) are 10x as effective as troopers (BOBs, etc.), and are retrievable after combat. Troopers are not retrievable. Also, marines and troopers must be used to take over a colonized base.