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Whatever happened to the research module must have spread to the other ships. We have no choice but to deal with them as hostiles. Get a research team studying the tapes and stay away from the research modules at all costs.
As soon as you regain control, open up the research menu by pressing the R button. Select "infection organism" and begin researching. If you haven't already (which you should have, if you followed the steps in this walk-through), start moving the Kuun-Lan to the middle of space to the resource patch. As mentioned in the objective, stay away from the research module. While you are researching infection organism, open up the Kuun-Lan's build menu (by pressing the B key) and replace your infected ACVs.
Destroy any infected ships that attack while you review the tapes to learn more about what happened to the Clee-San. However, stay away from the research module, as it will probably infect anything that gets near it.
Continue harvesting the remaining resources. Defend the Kuun-Lan and attack the infected ships. Place ACVs in aggressive tactics and in X or claw formation, then bandbox attack the incoming infected fighters. The new enemy will send out workers in an attempt to harvest the remaining resources - where the bulk of your fleet should be. If your Kuun-Lan rests here, as it should, its firepower will help defend your own resource group as well as the ACVs.
Eventually, a group of raiders jumps into the battle area to take the Clee-San - the raiders are unaware of the new alien threat. Continue to defend the Kuun-Lan from attack. The attacks will become stronger and stronger. Keep your vessels near the Kuun-Lan and consider docking the ACVs that are heavily damaged. Soon, you'll be ordered to hyperspace out of the mission area. All ships must dock or be lost before the hyperspace jump can take place. Wait for the ships to dock, then prepare for the next mission.
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