Covert Operations (EU2012)
Source: XCOM: Enemy Within DLC
Dealing with EXALT
Anti-EXALT operations are accessed through the Covert Operations view, which becomes available in the Situation Room after EXALT becomes active. There are 2 main ways of dealing with EXALT: Intel Scans and Covert Operations missions.
Intel Scans will reveal all hidden EXALT Cells cells present on the world. The first Intel Scan taken each month has a fixed cost of §50, with later ones increasing by 100% of the previous cost. On Easy difficulty level the increase is only 50%.
To stop a revealed EXALT cell, XCOM may perform a Covert Operation on the country where the cell is based while the cell is still exposed (from 2 to 7 days, depending on difficulty level). There are two types of covert missions: Covert Extraction and Covert Data Recovery, with about 10 maps for each type (20 total). There's no Meld present in Covert Missions maps. There is also no way to know which type of covert mission you will have before the Covert Operative is deployed.
The operation consists of two steps, first the insertion of one of XCOM's soldiers as a Covert Operative (through the Situation Room) and 7 days later its extraction through a tactical mission. If the tactical mission is ignored after the XCOM soldier is inserted, the Covert Operative will be lost as KIA. If the Covert Mission is a failure the EXALT cell will disappear and go into hiding into another country.
Besides elimination of the EXALT cell, success in the mission will provide a clue about the location of the EXALT base, and -1 panic to that country. Deploying an Operative will also prevent that country from leaving the Council at the end of the month, if its panic level has reached 5.
EXALT Base Location
Every successful mission where you recover EXALT intel will give a clue about the location of the EXALT Base. In the Covert Operations menu, you can read the clues, as well as markings on the countries that have been ruled out (and don't worry: it's automatic, so you don't need to hit Wikipedia for population statistics or Civ 5's civilizations) Once you get 3 clues you may make an accusation (raid) against a country.
- If the accusation is correct then you'll be able to assault their base and end their menace for good.
- If you're wrong the country will leave the Council.
- If you accuse a country which already left the Council, the penalty for guessing wrong is a continent-wide 2 point panic increase.
- If all of the continent's countries already left the Council there's no penalty added for a wrong accusation. This can be used to narrow down the EXALT Base choices.
- Failing to destroy the EXALT base during the raid mission will also cause the country to leave the XCOM project or raise panic on the rest of the continent by 2 points.
Note though, that while 3 clues acquired will allow you to assault the base, with three clues gained, you will have eliminated only half the countries, leaving eight to choose from. It will take approximately 7 or 8 clues total to eliminate all the countries except one.
WARNING: After activating the Gollop Chamber you will no longer have the option to assault the EXALT base.
Regular Covert Operations to keep EXALT neutered means more experience points for your soldiers, extra credits, additional cool looking weapons (to be sold or used) and less hassle for XCOM.
There is value in keeping EXALT alive, allowing you to "farm" them. Since EXALT never progress beyond laser weaponry, they're a comparatively easy way to get soldier experience compared to end-game aliens. Late game you can become almost EXALT-proof by having enough labs to neutralise research hacks, enough income to make sabotage inconsequential and responding to propaganda operations to bring the panic level down again, meaning there's no great pressure to finish them off.
EXALT Base Clues
The game automatically eliminates the countries described on the clues so it isn't necessary to figure out by yourself which countries are described or not.