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Covert Ops ships in Eve are designed for intelligence, and nothing but intelligence. They, unlike the vanguard ships, do not have to get into fights, and generally interfere with the ships of the enemy. Covert Ops ships are directly engaged in the exploration of various highly secure facilities and objectives, which without invisibility can be "explored" only with a very powerful fleet. Covert Ops ships quietly explore moons with POS, scan the open space for enemy ships and then direct the main fleet to them. Their specific feature is a quick scan with scan probes.
There are only 4 ships in the game that can be used as Covert Ops ships - one from each race.
In fact, it's possible to use other ships as well for such operations by installing modules Covert Ops Cloacking Device II (Cloaking Device). Such ships will have several times lower speed,  and lower speed of probes scanning, but they will have much more firepower, some tanking and even tools for electronic warfare; and so they can attack single targets and hold them until the main fleet arrives, or shoot the target down on their own.
Recons are a transition link between the specialized Covert Ops ships and avant-garde ships. Their invisibility allows them to perform the functions of researching moons, and in particular explore what is behind the gates no worse than the specialized Covert Ops.
Covert Ops ships can also be used as beacons, that is be used for positioning the major forces of the fleet before the actual battle. Or they can fly along with smaller attack forces to quickly scan the cosmos and find targets. The ability to quickly scan the space can be very useful in combats near asteroid fields, or when searching for possible ambush at gates. Their high speed makes Covert Ops ships indispensable for finding various options for re-dislocation and movement of the fleet.