Maelstrom: The Battle for Earth Begins is set in 2050 in a post-apocalyptic future following an ecological disaster which results in much of the planet's submersion, as well as the subsequent nuclear holocaust over the remaining resources.

Most of humankind has taken refuge beneath the surface, taking shelter from a long-standing war between the guerilla-warfare Remnants, and the hi-tech Ascension.

In the midst of this war, an alien race facing extinction, known as the Hai-Genti appear, quickly flooding the land and slaughtering Remnants and Ascension alike.

In Maelstrom: The Battle for Earth Begins, the player can also control the hero units directly, in third person perspective.

Players can take control of a faction's hero unit, and play the game from a third-person perspective, giving a significant advantage in range and sight, as well as the ability to launch a pre-emptive strike.

The Hai-Genti cannot terraform, but instead flood the map by means of Mutagen pumps, giving them an advantage in early game against vehicles.

These Havens provide an infinite source of Salvage, and act as a construction site for the middle man Scavenger, and barracks for all Remnant infantry.

The Ascension are the hi-tech remains of a corporation headed by Arlan Khan, who suffers from a messianic complex, and proceeds to command troops in a totalitarian manner, showing little concern for the dead.

The Ascension utilize hi-tech laser weaponry, advanced technology and raw firepower in place of unit diversity.

Unlike the Remnants however, DNA is harvested from Survivor compounds by means of a Manipulator, a unit which can perform terraforming like the scavenger, but cannot construct anything.

The Inception Spore can be evolved/upgraded, allowing for more eggs, which improve in size and Thrall capacity, as well as providing access to more upgrades.