Autocast is a feature that allows the player to delegate the use of special abilities to the AI. Most abilities begin with autocast enabled, and the player must turn it off if the feature is not desired. Right-clicking on an ability icon will target autocast on or off. A swirling animation will indicate when autocast is active.
When autocast is enabled, units will automatically use their special abilities, and the AI will select appropriate targets. Generally when certain abilities are set an autocast they will preferentially target capital ship, and will use it the instant the cooldown is over. A player can turn off autocast any time they want and take manual control if they want a specific target. The AI will not conserve antimatter and may not choose the targets (or time or place) that the player desires. This makes it useful to turn off autocast for abilities with high antimatter costs or that require careful timing to be effective. For some powerful level 6 capital ship abilities, it will sometimes target the weakest ship. One example of this is the Skirantra Carrier's Replicate Forces, for it has been known to replicate a Ravastra Skirmisher instead of one of your Skarovas Enforcers.
The Flak Burst ability of the Kol Battleship is an example of an ability that should usually be manually controlled. Abilities that cost less antimatter and don't need special timing, such as the Raze Planet ability of the Marza Dreadnought, can be safely left on autocast. Most of the time it is advisable to turn off autocast after major battles end and turn it back on just before the next major battle begins, to better conserve your fighting strength. Most capital ships are little more than oversized cruisers once their antimatter reserves are depleted.