The game takes place fifteen years after the original game. ( April 2020) ( Learn how and when to remove this template message) Please help improve it by removing unnecessary details and making it more concise. This section's plot summary may be too long or excessively detailed.

Where Homeworld was biased towards large fleets (as the player's main ship was a full-fledged mothership and the opposition was an empire of galactic scale), Cataclysm down-scales the fleets (as the player's main ship is a simple mining vessel and the adversaries are all limited in resources) In general, the main difference is the scale of fleets. The game also introduced new 3D features such as moving parts and transforming ships. The game's resource collectors perform the same functions that they did in the original Homeworld, however, when upgraded they can be used to capture enemy vessels, harvest crystals and repair friendly vessels functions that were carried out by separate, single-function ships in the first game.

Notable unit changes include the Processor, Cataclysm's adaptation of the Resource Controller, which has medium-strength weapons to defend itself, automated repair beams to heal nearby ships and four pads to dock with Workers harvesting resources. The player's Command Ship is now capable of attack though slow, the Command Ship is capable of delivering a high amount of firepower, most notably the Siege Cannon capable of crippling an enemy Command Ship with a single well aimed shot. Though it uses the same engine as its predecessor, several changes were made such as: the ability to toggle time compression between normal speed and eight times faster ship upgrades (improving armor and adding new abilities), Command Ships and Carriers are given the ability to add external modules for ship research and fleet support fuel was eliminated from the game and finally the sensor display could be used to issue attack orders to units.

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