Ion weapons deal ion damage, which disables systems by forcing power out of them. Ion weapons are blocked by shields, and the ion damage is applied directly to the shield system instead of the targeted room.
Ion weapons do not damage hull, systems, or crew. They can only be shot down by Mark II Defense Drones.
How ion damage works
Each point of ion damage forces 1 power out the system for 5 seconds; the power is returned to the reactor. While under the ion effect, the system is "locked" so that power cannot be added or removed. When the ion timer expires, the system is "unlocked" and functions normally. The ion timer is limited to 25 seconds, but there is no limit to the amount of ion damage that can be applied to a system, meaning that any system can be completely disabled with enough ion.
The ion timer is shown by a light-blue "ticking clock" circle overlaying the system icon, with a number in the middle. This number represents the 1/5 the remaining ion time (for example, "3" represents 15 seconds). This number is also equal to the amount of ion damage applied to the system, unless it received more than 5 ion damage.
When an ionised system is hit by more ion damage, the ion damage stacks: it forces more power out the system, and adds to the current ion timer, keeping the system locked down. Some ion weapons fire quickly enough that they can self-stack: their ion damage will not wear off before the next shot arrives, so they can disable a system completely by themselves (usually shields).
For example, an Ion Blast 2 fires every 4 seconds for 1 ion damage (lasting 5 seconds). Provided it does not miss (and is not delayed by a long cloak), this weapon can completely disable any number of shields. Whereas a Heavy Ion fires every 13 seconds for 2 ion damage (lasting 10 seconds), so by itself it can only disable 1 shield layer.
Tips and nuances
To learn how ion damage works, try fully upgrading your sensors and manning them. This allows you to see the power allocation and ion timers on enemy ships.
Multiple ion weapons can be combined to disable systems more effectively. A single Ion Blast 2 can theoretically take down 4 shields, but in practice this will be ineffective against enemies with high evasion or a long cloak. Adding another ion weapon makes it faster and more reliable, because you can afford to miss a few shots before the ion damage wears off.
Zoltan Shields take double damage from ion weapons. The power provided by Zoltan crew is unaffected by ion damage. For example, two Zoltans in the shields room will always power one shield layer, no matter how much ion hits the shields.
Subsystems (such as piloting) do not use power but are still affected by ion damage. Zoltans cannot protect a subsystem from ionisation. While a system is ionised, it cannot be manned by crew (even Zoltan crew).
The weapons system responds differently to ion damage, due to how weapon power works. Even a single point of ion damage will take a weapon offline, forcing all that weapon's power out the system (but still only for 5 seconds). Hitting the weapon system with multiple ion shots can disable multiple weapons, regardless of how much power each weapon uses.
When ion damage is applied to cooldown systems (such as cloaking), it adds to the current cooldown timer. Hacking behaves differently, due to a bug: ion damage will interrupt an active hack and reset the current cooldown to the amount of ion damage. This means that stun-bombing your own hacking while it is on cooldown will shorten the cooldown to 5 seconds instead of 20 (which may be considered an exploit).
List of ion weapons
Ion Blast
Ion Blast
"Ion weapons can disable systems without causing hull damage."
- Costs 30
- Fires 1 shot with 1 Ion damage.
- Has a low chance to stun crew (Advanced Edition).
- Requires 1 power and takes 8 seconds to cool down.
- Two of them come equipped on Noether.
- Cannot stack ion damage by itself, except with full crew skill and 3 Automated Reloaders.
Heavy Ion
Heavy Ion
"Ion weapons can disable systems without causing hull damage."
- Costs 45
- Fires 1 shot with 2 Ion damage.
- Has a low chance to stun crew (Advanced Edition).
- Requires 2 power and takes 13 seconds to cool down.
- Comes equipped on The Vortex.
- Cannot self-stack, except with full crew skill and an Automated Reloader.
Ion Blast Mark II
Ion Blast Mark II
"Ion weapons can disable systems without causing hull damage."
- Costs 70
- Fires 1 shot with 1 Ion damage.
- Has a low chance to stun crew (Advanced Edition).
- Requires 3 power and takes 4 seconds to cool down.
- Comes equipped on The Torus.
Hint: fires faster than the stun count-down, thus can be used stand-alone, provided it does not miss.
Boss Ion
Boss Ion
"1 damage ion 3 shots."
- Costs 40 (cannot be bought or found)
- Fires 3 shots with 1 ion damage each.
- Requires 1 power and takes 28 seconds to cool down.
- This is one of the weapons the Rebel Flagship uses. Can only be acquired via modding.
Advanced Edition Ions
Ion Stunner
Ion Stunner
"Ion weapons can cause system damage without causing hull damage. This ion weapon stuns crew inside the room for 5 seconds."
- Costs 35
- Fires 1 shot with 1 ion damage.
- Requires 1 power and takes 10 seconds to recharge.
- Stuns all crew in affected room for 5 seconds; this includes crew in the shields room if the shields themselves were hit.
- Comes equipped on The Swallow and Kruos.
Ion Charger
Ion Charger
"This ion weapon can charge multiple times, giving it additional projectiles."
- Costs 50
- Fires 1-3 shots (based upon charges) dealing 1 ion damage each.
- Requires 2 power, gains a charge every 6 seconds, can hold 3.
- Comes equipped on Cerenkov.
- If the autofire setting is on, it will fire a charge as soon as it is gained.
- Can bring down shields if manned by skill 2 crew and does not miss.
Chain Ion
Chain Ion
"This weapon's Ion damage increases each time it fires to a max of 4."
- Costs 55
- Fires 1 shot, with each subsequent shot dealing 1 additional ion damage, up to a maximum of 4.
- Requires 3 power and takes 14 seconds to cool down.
- This weapon does enough ion damage per second (ion stun duration is dependent on damage) to bring down any shields, unmanned (if it does not miss).