A compilation of what the ISSF ship abilities do:
Scan
The probe does an extensive scan of the system. Similar to the Probe ability.
Disable Shields
A well-placed shot knocks out an enemy ship’s shield array.
Hellfire Missiles
Gives a burst of increased fire rate of missiles, effectively dealing a heavy amount of damage.
Nuclear Warheads
Highly destructive weaponry increases the damage output from the using ship.
EMP
An electromagnetic pulse quickly disables other ships, but is only effective at short range.
The Rottweiler EMP is powerful and knocks out target ships for a long time, but needs to recharge for an equally long time in order to fire it again.
The Valkyrie EMP has proportionally shorter time than the Rottweiler, but is effective enough to escape a pursuer.
Repair Crews
Skilled repair teams sent to damaged ships quickly keep them in operation.
Ammunition Supply
A constant stream of ammunition replenishment keeps a high firing rate for the ships being supplied.
Seek-and-Destroy
The using ship receives a boost in speed to close the gap and deliver a crippling blow fleeing ships.
Ping
Ship emits a powerful signal that detects the smallest of ships through the most powerful radio emissions, thus identifying cloaked ships.
Boxer Missile
An anti-ship missile powerful enough to destroy a frigate instantly.
Emergency Power
The user ship’s power is redirected into its weapon and shield systems, increasing the ship’s firepower.
Blockade
The ship blocks trade to and from the enemy’s planet thus stealing the enemy’s credits. Ability’s effect increases in the presence of trade ports and refineries. Has similar effect to Embargo.
Moment of Desperation
As a last-ditch action, the ship’s captain orders the ship to ram the closest enemy ship. This action severely damages and possibly destroys the using ship, but guarantees that the target ship is destroyed. (This ability will be limited to only when the ship's hull is damaged beyond half-way)
Flak Screen
A screen of flak-fire is used to destroy any small ships or fighters that dare too close to the ship.
Evasive Maneuvers
The ship receives extra power to is engines, allowing it to outrun incoming ships and evade some weapons.
Scramble Fighters
An extra squadron of fighters is launched to counter a force of fighters and/or bombers.
Perseverance
Repair crews work against incoming attacks, keeping the ship in the fight longer.
Fire-Control Array
Allies receive an extended targeting range and increased accuracy.
Missile Screen
A point-defence system protects the ship and its nearby allies from long-range missile strikes.
Propaganda
The ship broadcasts a radio signal to the occupying faction of the planet, increasing the planet’s allegiance to the ship’s user.
Sensor Jammer
Enemy ships in the system cannot detect or target the user’s ships; effectively cloaking them from enemy radar. This is a toggled ability, but ally ships must be within range in order to be covered by the jamming system.
Gauss Rail Gun
A high-power kinetic energy weapon capable of ripping a hole through a ship. (same as Kol's)
Missile Storm
A cloud of missiles is all launched at once, randomly hitting anything in range.
Thermonuclear Warheads
Increases the destructive power of missiles.
Cluster Bomb
A timed explosive missile is fired where it will detonate, filling an area with a devastating amount of damage.