Having had to depend on an Ion/Beam combo, I've worked out the Critical thing for Ion Weapons is consistency.
As agent86's answer says, Multiple hits within the "Lockdown" period stack, but the minute that timer runs out, the locked system restores to full.
So your aim is to keep the lockdown timer on any disabled system from running out. Therefore you should be focused on ensuring on repeatedly hitting one system within its period rather than spreading ions around other systems.
To illustrate; if you bring shields down to 0 with ion, then target weapons, you have to hit the shields again before the lockdown on the shields lifts, otherwise they'll restore, and then while you're bringing them down again, the lockdown you've put on the weapons will lift.
If instead you keep hitting the shields, you'll keep resetting the lockdown timer on them and they'll stay down. At this point your other weapons pick up the slack and tear into the non-ionned systems.
Once you have low enough shields that other weapons can penetrate (e.g. your lasers can bring them down, or your halberd/glaive can breach them), you want to focus at least some of your system damage on the helm and engines. Remember, every miss with an ion weapon is bringing you closer to a timer reset.
One useful trick is to alternate between ionning a single system and the shields (e.g. one to the shields to reset their timer, then one to the weapons to lock them down). However you increase the chance that one miss will lead to the shield lockdown running out, especially with the slower Heavy Ion cannons. (Which is why faster ion blasters are more expensive/require more power than ones that do more damage).
Other useful tips:
- Even after a lockdown lifts, weapons and shields still need to recharge their buffers.
- Lockdown damage and real damage doesn't stack.
- The Cloak time is longer than the Ion Timer, so cloaking is a great defence against Ions. How much of a problem this is depends on your Ion capacity and the enemy shields, but you need to disable it. Got into a complete stalemate with the boss based on this...
I hope this helps!
The only way to close your doors is to repair the "doors" system (appears as a vertical equals symbol). It only has to be repaired one point to allow you to close all doors. This will be very difficult to do in your situation as your crew may die of oxygen deprivation before they can make it to the door control and perform the necessary repairs. In this case you appear to be beyond all hope.
Best Answer
Experiment Setup
I moved my whole crew up to the front of the Red-Tail, and evacuated the back half of the ship, leaving oxygen in only the three front rooms. This reduced my oxygen total to 20%. Then I closed doors and started timing every 10% increase.
Results
First I closed all the doors. Each 10% increase took 9.7, 10.5, 10.6, 10.2, 10.2, 10.6, 10.0, and 10.6 seconds. So it's very slightly less than 1% per second (1% per 1.03 seconds or 0.97% per second, possibly from 0.96% per 1 second which is a common math error when programming a game that runs at 60Hz).
Next, I closed only the outside doors, and opened all the inside ones. This took 66.3 seconds (8.2; 8.3; 8.3; 8.4; 8.2; 8.2; 8.3, 8.4). So oxygen does diffuse (faster?) through open doors. The background of the previously pressured areas turned slightly pink.
Next, I opened all the doors between depressurized areas but left closed the doors in the front which were still pressured. 82.6 seconds, basically the same as my first test.
Finally, I depressurized only the back three rooms of the ship, turned off my O2 generator, closed the outer doors, and opened all the inner ones. The three back rooms re-pressurized despite my generator being turned off until they equalized with the rest of the ship, which was also steadily losing oxygen; eventually the whole ship depressurized.
Conclusions
This behavior is explained by a model where the O2 generator works by supplying a fixed amount of oxygen to each room per second, oxygen is naturally consumed slower than this replenishment, and oxygen diffuses only between open doors. This means if a room with a high oxygen level has an open connection to a room with a low oxygen level it is giving oxygen to that room and receiving replenishing oxygen from the generator nearly as fast as it is giving it up and the other room is receiving oxygen from the generator, resulting in overall faster replenishment. If the doors are closed the new oxygen in the already-pressurized room is just "wasted".
Because the oxygen level required to keep your crew alive is fairly low it's often good to open doors to help re-pressurize areas faster assuming your oxygen generator is working.
FTL's model of oxygen seems to match our intuitions about how fixed volumes of gasses in an enclosed space work.
One interesting prediction of this model is that a sufficiently long path length of rooms may make it possible to survive indefinitely with a working generator despite a door open to hard vacuum. I've been testing this prediction on the Osprey for several minutes now, and it seems to be true.
If I open the second door on the top left, the room Mr Buga and Liam are in de-pressurizes. If I close it but leave the top one open, it re-pressurizes.