Strength affects two factors, the damage you cause with Meleé attacks and your inventory space. For every point of strength you have, you gain 3 extra inventory spaces, enough for one weapon, or three items. Strength is important for Marines, because of the many different types of weapons that they need to carry. OSA agents, on the other hand, have little use for Strength because they only need their Psi Adapter and a Pistol, not needing to lug around many types of weapons or the Ammo for them. Strength also determines whether you are able to use the heaviest armor, and a couple of the biggest weapons. I recommend getting 4-6 points of strength if you are a Marine, 3-6 if you are a Technician, and 2-4 points if you are an OSA agent.
Endurance gives you hit points and determines your resistance to radiation and toxins. There are better ways of gaining a resistance to radiation/toxins, but the hit points are nice, so put a couple of points here.
Psionics affect the power of your psionic abilities. Put as many points in here as possible if you use psionic abilities a lot, if you use one or two spells only, 2 points is fine. If you never touch psionic abilities, don't put any points in this.
Agility increases your running speed, reduces fall damage, and reduces weapon kickback. You'll want to put some points in to this, no matter what class you are, for the increase in running speed increase. With enough Agility, none of the Meleé range attackers will be able to touch you. The reduction to fall damage isn't really helpful, as there aren't many areas you can fall from that will cause damage in the first place, while the reduction to Weapon Kickback helps with the stronger weapons which tend to have stronger kickback. Marines should have this maxed out, OSA agents should have 3-4 points, and Techies should have this anywhere from 3-6 depending on how they're playing.
Cyber Affinity (Labeled simply "Cyber" in your MFD display) eliminates one filled node for each level of Cyber Affinity you have during any Tech Skill "hacking" sequence. It doesn't become too helpful until about halfway through, and really only if you do a lot of computer hacking. However, near the end of the game, you'd better have some points in this skill if you plan on doing any hacking at all as sometimes entire grids can be filled with white nodes unless you have some Cyber Affinity.
This is one of the more powerful skills in the game. Having a high hack ability allows you to hack into the many Security Stations across the Vaun Braun and Rickenbacker, disabling the cameras, and more importantly, any turrets. When you've disabled the turrets, you're able to approach them, and with a level 3 hacking ability or higher, you can actually gain control of the turret. Considering that most turrets are in important areas, they can be a great help.
This is a completely useless skill. As long as you keep an eye on your maintenance level for you weapons, they won't break down. And in the rare event that they do break, there are plenty of auto-repair items that can fix it right back up for you. The same goes for weapons that you find. If you find a really good weapon that you just want to try out, but can't wait till you find an unbroken one, just use an auto-repair item instead of wasting your upgrade points here.
This is a moderately useful skill. I'd recommend getting level 1 or 2 in it so you can modify the pistol, shotgun, and laser pistol to level 1. After you've modified them to level 1, simply use a French Epstein device to upgrade them to level 2. It'll be well worth the handful of upgrade points you spend. However, I wouldn't recommend upgrading skill past level 2, as you'll find plenty of French Epstein devices to upgrade your weapons to level 2 if you're judicious in their use.
This is another very important skill. Every weapon in System Shock 2, with the exception of the melee weapons and the Psi Amp, has a maintenance level. When a weapons Maintenance level gets to 1, there's a chance with every use that the weapon will break if you use it. Having your gun break in the middle of a fire fight is not fun. Try to get this up to level 4, because at that level you can perform maintenance on every weapon and you'll raise the maintenance level on a weapon by 4 with every use of a maintenance tool, which will save you a lot of money. In addition, the maintenance skill raises the maximum you can charge stuff to, which will help save you trips to the recharge station and back.
There's some use in this, as it allows you to use certain items, and give you bonus damage against enemies. However, the only benefit from putting more points in this is lowering the time required to research. Instead of putting your points in here, just equip the lab assistant to get level 1 research, and run off and continue with your mission while your research takes place. Then put the points you saved towards a more useful purpose.
The standard weapons skill is the most important Combat skill. Your first weapons will be fall under the Standard category, and all of the Standard weapons are quite useful. If you get this up to level 6, you'll be able to use the Assault rifle, which is the best weapon in the game. Investing your points here is both a good short and long term investment.
Energy weapons are the most effective weapon class against mechs. However, the laser pistol is the biggest reason to put points into this skill. It's extremely effective against all robot class enemies, and is moderately effective against most flesh based creatures as well. This is another weapon skill that will serve you well throughout the game.
The only reason you should bother with this class at all is for the grenade launcher. It's a powerful weapon, and ammo for it is very plentiful. However, because the other weapons in this skill as so worthless, and because the grenade launcher already does plenty of damage, there's not much reason to get more than level 1 or 2 in this skill level.
The exotic weapons class is a major disappointment. All the weapons show up too late to be useful, and require not only Exotic Weapons skill, but research skill as well. Of special note is the ammo that the weapons in this class use. Throughout the game are many various empty glass jars. For the longest time, I couldn't figure out what they were for, I figured they were just clutter like the plants scattered throughout the game. Through trial and error, however, I found that the glass jars are actually ammo containers for the exotic weapons. By dragging an empty glass jar from your inventory on to one of the many flat annelid pools throughout the game, you can actually fill the jar with annelid worms which can be used as ammo for your exotic weapons. Nice of them to explain this somewhere. The only redeeming thing about the exotic weapons is the Crystal Shard, which is the most powerful melee weapon in the game, however, by the time you find the crystal shard, you really shouldn't be using melee attacks. This class is just a waste, don't sink your upgrade modules here.
Damage from radiation and toxins reduced by 25%.
Extra 20% Benefit from all Hypos.
Adds three extra inventory slots.
Movement speed increased by 15%.
Each shot with a ranged (Non-Psionic) weapon does 15% more damage.
One time bonus of 8 Cyber Enhancement Units.
Allows the use of two implants at once.
Increases maximum hit points by 5.
Increases all hand-to-hand damage by 35%.
+2 hacking skill (If you already have at least 1 point of skill) applied only to security computers.
You can execute overhand attacks with Meleé weapons.
You can extract a diagnostic/repair module from any destroyed robot. You can use this item to heal 15 hit points.
All items in replicators cost 20% less.
Psionic burnout no longer damages you.
Nanite cost for making weapon modifications is 50% cheaper.
Automap for each level is automatically filled in.
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