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So I've gotten my first supply retaliation in a high advent strength region (Advent strength 7, formerly held the Blacksite). The objectives for the mission are:

Protect the Supplies,
Neutralize all Enemy Targets

Except, as far as I can tell, no aliens spawned on the map. Instead huge pods of enemy reinforcements are being warped in every two turns. I've wiped them out multiple times, so that there were no aliens left on the map, but the reinforcements keep coming. Did I miss an enemy pod in one of the corners of the map? Am I supposed to call a Skyranger for Evac? Is there a limit to the number of reinforcements/number of turns that is not shown anywhere? Or was this mission supposed to be unwinnable?

This is the latest turn, with a group of reinforcements just that just spawned (and 7 died in my overwatch trap as they spawned in): http://imgur.com/FhF0ZzL

Also, can I instruct the rebels to forget the supply and grab the bodies? I think I've fragged at least 40 aliens so far and the bodies are worth more supply on the black market than is in the convoy anyway.

That's how supply retaliations work actually. You have a limited number of double RNFs that you have to defeat. They drop every 2 turns in 1-2 pods, number of waves depends on region strength, most likely. Usually it's 3 to 6 waves. You can evac prematurely if you feel overwhelmed. Most players believe supply raids the easiest and treat them as XP farm.

Oh ok, thanks for the reply. Can you add an indication for how many enemy pods are remaining, or change the mission objectives to Survive?

Otherwise the mission objectives are going to conflict with the Intel Retaliations, where there are aliens already on the map and you have to wipe them out.

Ok, looks like it's working as intended and that last group was the last pod.

Here's what happens when Advent REALLY wants to take your supplies: http://imgur.com/Z47uHV8

Wow! Good job commander, the aliens will think twice before knocking on your door again.