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The Core Contingency introduces 25 new campaign missions: 12 sequential missions for each side as well as a bonus mission for the Arm. The campaign resumes the plot where Total Annihilation's campaigns ended. The Arm has emerged victorious from its 4,000-year war with the Core, and taken over the galaxy. However, a lone Core Commander, hidden away in a distant star system as a contingency in case the Core were ever defeated, has survived. This Commander has been given one mission: To use an ancient alien Implosion Device to destroy the entire galaxy and the Arm in the process, remaining safe inside the device and emerging to rebuild the Core once it has finished. The Arm gain knowledge of this plan and set out to prevent it from ever reaching fruition.

In addition to the new campaigns, The Core Contingency adds a multitude of new units, structures, tile-sets and features. Notable additions to the unit roster include hovercrafts, seaplanes, amphibious K-Bots, rapid-fire plasma cannons, pop-up defenses and the enormous, powerful Krogoth super K-Bot for the Core. Several new, unique tile-sets were added, including a water-covered planet (which prompts the use of new naval structures and seaplanes), an urban environment, a planet with seas of acid, a planet with a crystalline crust and many others. These tile-sets can be found in the 53 added multiplayer maps, and manipulated in the added map editor.

The expansion also fixes many of the issues and glitches found in the original game, and adds all of the units released for download by Cavedog.

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