Should your team decide to spare Tanaka's life, he informs you the best way to kill the infested is to flood the ventilation system with a deadly Bio-Toxin he created. In theory it will kill any biological life that comes in contact with it. Alpha Company themselves are protected by their Power Armor, but the Civilians still alive on Apollo are damned by this course of action. Their loss of life is worth saving the colony, and possibly humanity as a whole.
Alpha Company proceeds into the ventilation mainframe located just inside the Scrapyard entrance. They must stand on the Hexes around the mainframe until the Toxin's release is completed. Afterwards, they must quickly move to a safe location. A massive horde of infested awaken, and will almost certainly overrun alpha co if they stay too long.
Unfortunately, the Infected are stronger than hypothesized and the Toxins do not kill many of the larger infested. Many of the weaker zombies are driven into the underground mines, or into the Bio-Domes.
Afterwards, the team will have a minute or two to prepare themselves for their climactic battle against Ivax.