Subset Games Forum

The best way to deal with it is to not deal with it. The hack hits a random room, so if it hits something crucial like weapons, jump away asap and jump back. Best case scenario is it hacks something entirely nonvital like Sensors. Medbay and Oxygen (assuming you have level 2 Oxygen, otherwise it'll kill you) are also good ones. Note that if the Flagship is on the base, you can only do this once before the timer makes you lose anyway.

Another way to deal with it is to go into the fight knowing you'll be facing it, which you can now do every time.

If you have a defensive (or anti-drone) drone, you can fairly reliably shoot it down. And they're good in general against the boss.

If you have hacking, you can wait on it and hack their hacking if they hack something good. Otherwise, hack shields. Bonus, hacking their hacking makes them take forever to get from the medbay to the front of the ship.

If you have as many systems and subsystems as possible, you maximize the chances that they'll hit a nonessential system. That battery may save your run even if you don't need it.

And as @Gabriella said, "run away" is always an option. I'd say, if you don't have hacking or defensive drones, b-line to the flagship as quickly as you can to maximize the number of times you can run away if they hack something important.