The best way to deal with incoming UFO's is to camp outside the dimension gates, once you get the funds, sort out 3 fleets (prefferably with thier own base just for ease later in the game), have each fleet at each dimension gate (not directly next to the dimension gate as both aliens and your ships have a tendancy of blowing up buildings and managing to kill all other vehicles).
Check every few hours or so to make sure the gates are nearby your fleets and the gates havent moved, then once the aliens strike just launch out your fleets at the UFO's, generally the UFO's only come out of one gate so get your spare fleet to either split and assist both other gates, or go for the highest priority target first.
Your highest priority should be infiltrating capable ships such as the early scout, the transport, assault transporter etc...
Then secondary objectives of the escorts i.e. alien probe, alien escort ship etc..
Check infiltration graphs and try and deduce buildings aliens have infiltrated by looking at previous infiltrations of buildings and see if the suspected corps are nearby, aliens move from building to building.
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