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i think an anti-drone drone might disable a hacking drone but i haven't tried.
For your particular situation here, upgrade the O2. There are options if you can't, but this is the simplest solution that's cheap and works to the point many of us do it before the end for the sole reason of countering this if it happens. The other options would be jump away (but you risk something worse), kill the system (but that's precious firepower), sit in the medbay (not always viable)/teleport over to the enemy ship, or just finish the fight very quickly.
Overall answers to hacking include things like defense drones (they will eventually run out of parts, or you can try to let the hacking drone through at a harmless system; also works better with cloak if their missiles are distracting your drone), hacking them back if absolutely necessary (usually better to hack something else), breaking the system, just generally having enough redundancies and buffers that any single system being disabled won't be a disaster.
The flagship's hacking system is the most random part of the battle, and it encourages you to have a more well-rounded ship than normal so that you're not necessarily tied to any one of your systems for success. Here's a few ways you can mitigate its threat:
1) Outfit your ship with a full arsenal of 8 systems + 4 subsystems. This means buying Sensors, Door Control, and Backup Battery on any ship that doesn't start with them, even if they're not vital for your success. (Whether they're worth the scrap cost or not will depend on your specific playthrough and preferences.) By having a full 12 system count, this gives the flagship more potential targets to choose from, and it increases the likelihood that it targets something unimportant like Sensors instead of something vital like Shields.
2) Remove all reactor power from non-vital systems (Teleporter, Mind Control, Hacking, etc.) the moment the flagship battle starts, so that if the flagship hacks one of those systems, you don't have to worry about it also locking reactor power in them. Make sure that you NEVER have a crew member stationed in the Medbay at the start of this encounter (or any other encounter, really).
3) You can *try* to shoot down hacking drones with a Defense Drone of your own, but it's arguably not worth the risk against the flagship. DDs don't have 100% accuracy, you won't be able to deplete the enemy's drone supply before it fires its missile launcher, and when the missiles are fired at your ship at the same time as a hacking drone, then it's very likely that the DD will target a missile and let the hacking drone pass through. It's arguably *less* risky to just let the first hacking drone pass through unobstructed, as this will cause the flagship's hacking duration to overlap with its cloaking duration almost completely. This actually lessens the threat of having your weapons system hacked because your weapons wouldn't have been charging during the enemy's cloak time anyway. If you *do* want to roll the dice and attempt shooting down the hacking drone, try using multiple defense drones and/or a Defense Drone Mk II, and cut the power to your DD if you can tell that the hacking drone is targeting a non-vital system anyway.
4) Be willing to jump away from the fight if the flagship hacks a vital system, hoping for a more favorable roll when you return to the battle to try again. This means that you need to intercept the flagship before it's docked at the Base for too long, so that you have enough turns remaining to bail and try again. (I personally like to initiate the flagship fight when there are precisely 2 turns remaining, as this gives me a substantial number of jumps to collect scrap throughout sector 8 while still allowing me 1 chance at a re-roll for the flagship. If your ship is already sufficiently upgraded by the time you reach sector 8, consider intercepting the flagship as soon as possible for even more wiggle room.)
5) If the flagship hacks a vital system on your ship and you have no remaining turns to jump and retry, use your own hacking system to counter-hack and eventually destroy the flagship's hacking drone, forcing a re-roll. This means that you can't be dependent on your own hacking system for disabling something else on the flagship, though. Be very stringent on what you consider to be a "vital" system on your ship before you resort to something like this. You can probably get away with having your Piloting or Engines hacked as long as you have enough firepower to disable the enemy's weapons quickly, for example.
When the system is repaired to at least 1 full reactor bar, then you can hack it again.
A good time to upgrade O2 before the flagship is any time you enter a Slug sector, for the very same reason, because it effectively neutralizes the multiple suffocation events possible in those sectors. Also any time you get one of those super cheap upgrade a system options, often on the exit beacon for a sector, take it. O2 is one of the possible options.
It's actually a pretty good choice as you can abuse the Blast Doors that you can toggle for the enemy and pick off their crew 1x1 (hack room, teleport in, depower hacking to let the closest guy in (only 1), kill him, TP out due to cloaking).
Lvl 2 O2 is a must for the flagship and slug fights though... especially because Lvl 2 means you can shrug off a hit. Lvl 3 is not neccesary but can still be useful for the same reasons. (Lvl 2 also helps with dealing with breaches. Lvl 3 means you can completely ignore breaches basically)
Then again those super shields with their drones and maxed engines are the answer to every problem that the game can possibly present.
Hacking is just another system. I recommend playing around with it for awhile, and (somewhat obviously) learning the strategies on your own.
Responses to the above posts:
Counterhacking is awful. Needlessly wastes a drone part. There are ALWAYS more effective ways to cope with hacking. Always. If they hacked something really important, shoot their hacking system. If you enter a fight and find yourself either needing hacking to damage them or the enemy ship is well-outfitted, shell out the 8 scrap drone part.
It does, but very poorly. Defense drone is better for this.
Darn it mekloz. Stay in reddit.
Blah blah blah cut out all the boring stuff. Using DD's to groom the hacking landing system is a very good strategy, if you can spare the drone part. Also requires frequent pausing.
Also 3 Vulcans, a glaive beam, all systems maxed, 2 DD's, infinite generator power, and a pony.
Counterhacking is not the best strategy. It may be a decent one, but hacking always has a better application than counterhacking.