The US then leads a successful invasion on Iranian oil fields funding the toxin program, but it is soon learnt that Dr. Thrax has a secret lab at Mount Elbrus, and so sends a team led by Colonel Burton to destroy it and liberate prisoners of war along the way, while the Chinese operative, 'Black Lotus' gathers intelligence from across the river dividing the region. The US discovers from the documents that Dr. Thrax', a GLA General and scientist who plans to develop Anthrax Gamma Toxins. A US carrier group in the region provides aerial cover as US forces storm a secret GLA base, unintentionally discovering documents relating to 'Dr. The US then tasks itself with watching over the relief effort by the United Nations in Mogadishu, but GLA incursions make the relief mission difficult. A Chinese assault on the base had previously failed, so the US uses the powerful Chinese arsenal to overrun and destroy the missile silo using a B-2 Bomber. The GLA uses the Baikonur Cosmodrome to fire a toxin warhead at a US naval base in Northern Europe, prompting the US to respond before another missile can be fired. The beginning of the US campaign relates to the GLA's success in the previous game. The plot behind the Zero Hour campaigns picks up where it left off at the end of the previous campaigns. Unlike the previous campaigns, which were noted by Command and Conquer fans for not having full motion video cinematic sequences during mission briefing, the Zero Hour campaigns return to that Command and Conquer tradition, each showing a live-action video of a news reporter of the respective side giving details about the situation and instructions for what to do behind the current mission. Zero Hour contains 3 new campaigns of five missions each, one for each side, with their chronological order being USA first, Global Liberation Army (GLA) second, and China last.

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