The Core Contingency missions also feature native, hostile alien inhabitants of various planets, such as dangerously powerful sea creatures on the campaign's opening planet, Hydross, a water world. The level is available only in Hard difficulty, its highlight being experimental, super-powerful Krogoth Kbots which the player must overcome and whose production facilities the player must destroy. Krogoth Encounter is an Arm bonus mission, set during the time of the original game (and thus could technically be considered a 'lost mission') during the Galactic War on the metallic world of Core Prime, as the Arm was slowly making its way to domination. The Core Contingency expansion features 25 new missions, with 12 for each of its campaigns and a bonus mission, named 'Krogoth Encounter.' Meanwhile, rumors circulate amongst the mending Arm over the said Contingency Plan, so an Arm Commander is dispatched along with sizable reinforcements to confirm or eliminate the gossip. The Core Commander would stay inside the gigantic machine as it causes the galaxy to virtually self-destruct, then step out unscathed and rebuild the entire Core race. With modifications, the beacon could supposedly be converted into an Implosion Device-a single, phenomenally powerful superweapon which, when activated, would cause the entire galaxy to implode into itself, with the Core's pure intention to permanently extinguish the Arm. The Core Commander, the heart of the Core's Contingency plan in case the Core would ever be defeated, is charged with a single mission: to search for a powerful and ancient alien artifact hidden in the region.

However, a lone Core Commander survives, hidden away in a distant system. With the Core supposedly wiped out of existence, the Arm undergoes one-hundred years of reconstructing civilization. The Core Contingency picks up where the original game finishes with the Arm ending, in which the Arm achieved final victory over the Core in its homeworld Core Prime, in their Galactic War of over 4,000 years.

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