For an organisation to be taken up by Aliens they need an unit somewhere in one of the organization buildings. Aliens can't go around this, it must be done. What I usually do is check the graphs a lot and moniter infiltration very closely. I usually do everytime I finish a mission but most often than not it only take a second or two since I'm only spotting for organization with infiltration near 50%. Bellow 50% an organization is still pretty safe, above 50% you're in trouble and need to find that nasty Alien(s) who escaped your grasp. The trick is to find out where exactly the Alien(s) might be hiding.
More often than not if you are only a half decent spotter you will be able to see where exactly the UFOs beam down their friends. Once this is done the Alien(s) will usually try to infiltrate the attacked building but not all the time. Other times they will send small teams to also infiltrate adjacent buildings and speed is really the key here. The sooner you'll arrive with your team, the smaller the map will be (also influenced by the number of squaddies and Aliens on the map) and the smaller chance you will have for Aliens to get away to other buildings. Also do not forget that Aliens can flee the battlefield just like your squaddies. Sometimes they get away that way and flee to adjacent buildings.
So, what I usually do is to get to the city map and point at the last building which got Aliens beamed down to it. Then I select the half infiltrated organization so their buildings are highlighted on the map. If a building is near that point then it's pretty much that building you need to storm.
As long as there is Aliens in the building you storm then the organization won't mind much that you get there and kill them. If there is not, however, their standing VS you will drop a little each time you do this. It is worth checking all the buildings until you find the right one tough even if you need to make that organization hate you. You are there to defend the city after all, and you can always increase standing with donation money later on. It usually cost way less to bring an ennemy organization to like you than to try to get allied with one.
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