From an old update:
Let's start by giving you a specific example from one of the early quests and then go over the features. You need some energy cores, one of the scavenger crews has them, so you can either talk to them (pay a lot of money or con them like a pro), kill 'em all (always popular), or sneak around and do some breaking and entering.
There’s a built-in air purifier out back, you can use your Mechanics skill to open the hatch, making some noise in the process. If nobody comes to investigate, you enter the premises and TB stealth mode. The crew's leader is in the room next door, drunk after celebrating a successful run (if you come back later, he will be more alert). We check if he heard the noise. If he didn’t, he stays where he is. You need to make your way to a locked strongbox. Each step generates some noise, if he hears it, he goes to investigate. Finally, lockpicking the stronghold generates some noise too. So again, if he hears it, he goes to investigate. If not, he remains where he is and you get away clean.
If he does hear the noise, he goes to investigate, heading for the place where the noise originated from, meaning you should get as far away from that place as possible (as far as your AP allow, which means that sneaking will require high Dex and proper feats) or ambush him.
If he sees you (i.e. you're caught in his cone of vision), he goes for his gun, otherwise he starts searching. During the searching phase, if he comes close to you but doesn’t see you, you get an optional interrupt allowing you to insta-kill him using your trusted Critical Strike skill. Failing the attempt starts combat. You can also attempt to sneak up on him and kill him during your turn. If he sees you, he gets an interrupt attack and shoots you in the face.
1) Each action (movement, lockpicking, hacking, etc) is assigned noise points. The points, modified by your gear and Stealth) will add up with each action and will determine whether or not an NPC acting as 'guard' is alerted and goes to investigate.
So in this case you open up the hatch, the guard hears a light click but ignores it. You step inside, he hears something but ignores it too. You take several steps and finally get the guard's attention, raising his alert level. You success depends not a dice roll but on your skills and gear (either you can stay below the guard's radar or you can't). You can trigger his alert level the moment you step inside or when you make it to the strongbox and open it. Each subsequent action increases the alert level. A good thief can clean up the entire room, a not-so-good thief would have to stick to his objective and consider himself lucky if he isn't caught.
2) The movement’s noise points start at 1 and go up with every step (i.e. with every tile). It’s not that the third step makes more noise than the first two but the act of walking produces more noise than taking a single step (i.e. a single footstep may not be enough to trigger a guard’s attention but 3 footsteps might, plus it takes more skill to silently cross a hallway than to take a step or two). Thus more challenging tasks will require much higher skill levels and better gear. Same goes for optional objectives.
3) Your skills and gear will modify the noise points. For gear, we won’t go with % penalty but with +1, +2, etc. So if you wearing army boots with +2 and metal armor with +3, but your Stealth is 5, you generate 1+2+3-5 =1 points plus 1 with each step. Remove the armor and it will take a lot longer to make enough noise to alert the guards but if you’re caught, you’ll be wearing nothing but your jumpsuit.
4) Each guard's alert level is determined by his PER, something like 15-PER. So a guard with PER 8 will be alerted when you generate more noise points than 7. Thus the goal for the player is to have the right gear (not just the armor but the tools of the trade like jammers and electronic lockpicks) to reduce noise (if it takes you 5 min to open a lock, odds are you'll make more noise than someone who can open it in 30 sec). Overall, longer infiltration missions are much harder to pull off than shorter/simpler ones, which makes sense (without relying on higher checks, I mean).
5) In more open areas you can move freely during your turn. As long as the guards won't see you or won't become alert, you'll be able to get in and out without any problems. Getting caught doesn't always mean combat and painful, vividly described death. The exact outcome will differ based on each situation. Maybe your designated thief (can be you or any member of your crew) can talk his/her way out. Maybe the guards rob the thief and throw him/her out. Maybe they kill him or maybe they yell "we have your guy, come out!" and then you either come out and talk or leave him to his fate (to be killed).
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