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I recently reached the mission where you have to choose whether to cleanse a colony and side with the protoss, or try to save that colony and fight the protoss.

I chose to save the colony, that gave me +3 zerg research, and a nice cut-scene of the doctor leaving the ship and asking me to settle down with her.

What is the difference on that mission if one chooses to side with the protoss? Does this choice affect the story somehow? How does the doctor react?

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I left details out from the title on purpose to avoid spoiling the homepage. – jmfsg♦ Aug 8 '10 at 22:04
do you want the full spoilers, or only for the first choice? – alexanderpas Aug 8 '10 at 22:11
I haven't finished it yet, so if possible, only for the first choice @alex – jmfsg♦ Aug 8 '10 at 22:20

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The doctor wasn't only trying to save the colony but was also trying to save herself. She turned out to be half-infested already and the cutscene after the mission shows you dealing an infested version of her.

I didn't find any noticeable impacts on the decision I made aside from the bonus research though.

EDIT: Didn't notice this one. Apparently the reward is visual. WIKI

For Safe Haven (siding with the terrans) you get a banner from the refugees.

For Haven's Fall (siding with the protoss) you get a commemorative plaque from Selendis.

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