Damage is broken down into multiple types. Standard physical damage is caused by weapons, and will be displayed as e.g. "30-60 Damage". When an attack hits, the attacker rolls damage. The standard damage is rolled on one big die, so in the example of 30-60 Damage, that is a D31 + 29 damage. Gear, skills, buffs or Talents that increase the standard physical damage dealt by a weapon, do so by raising the maximum range that may be rolled. Note that they do not increase the minimum damage range. Thus equipping Shatter shells (+18 damage) to the above weapon, and using a higher level Talent (+42 damage) raises the roll to D91+29 damage.
Specialized weapons, gear, buffs or Talents may add special damage, such as Bio-Poison, Fire, or Plasma. In the case of special damage, the amount of damage is rolled as one big die, but this type of damage guarantees at least 30% damage. Therefore, if you cause 18 Fire damage with an attack, a D18 is rolled to determine the damage. However, by the 30% rule, the damage calculator will set the score to 6 if the die rolls lower than 6. All special damage is handled separately from standard damage and is soaked by Resistance and Res as opposed to Armor and Toughness. This technically means you have to deal with two sources of subtracting damage, but most foes have pretty low resistance.
For example, if a weapon causes 30-60 Damage, you roll D31+29. In this example the D31 rolls a 10 and the standard damage total is 39. For the example, the attack also causes 18 Fire Damage, which is rolled as a D18. Imagine the roll is a 14, (although even in the worst case case the rule of 30% would have set the Fire Damage at 6.) Entering the soak phase, the damage being caused is 39 standard and 14 Fire.
Sources of soak
Armor and Res generally come from equipment, although they can be enhanced by buffs.
Based on your class, you get additional soak bonuses for standard and special damage. All standard damage is additionally soaked by your Fortitude x Class multiplier, named Toughness. All special damage is additionally soaked by your Willpower x Class multiplier, named Resistance. These additional soaks function just like armor, where half of the soak is automatic and half is rolled on a big die, except that they cannot be penetrated and the values tend to be much lower.
Soaking Physical damage
Standard damage is resisted by armor. Half of the armor's protection is rolled as one big die and then reduced from the damage. Then, a penetration roll is made (D100 vs. Armour Deflection - Attack Penetration). If the D100 result is lower than the modified deflection, the attack does not penetrate, and the other half of your armor's protection value is subtracted from the damage as well. An armor with 24 protection will therefore soak up to D12 damage on a penetrating hit, or 12+D12 damage on a non-penetrating hit.
Toughness acts as a second layer of physical damage soak, but the values are smaller and it cannot be penetrated. Half of your Toughness is applied without any dice roll, and the other half rolled as a one big die.
Soaking special damage
Resistance and Res function in a similar way, but they do not have deflection values and cannot be penetrated (to make up for this, they tends to have much lower values than armour). All special damage is resisted by your standard Resistance, half of which is reduced without any dice roll, and the other half rolled as a one big die. Then, specific Res is applied, so Fire Dmg is resisted by Fire Res. Fire Res is basically armor for Fire Damage. If you have 18 Fire Res, you can soak up to 9+D9 Fire Damage.
The attack deals 39 standard damage with penetration 20% and 6 Fire damage. The target has 24 Armor with 80% deflection, 4 Toughness, 4 Resistance and 2 Fire Res.
The Penetration test is D100 against 60% modified deflection. The dice rolls 42, and fails to penetrate. The Armor soaks 12+D12 damage, and after the roll totals 16. 39 Damage - 16 Soak = 23 standard Damage. Toughness soaks an additional 2+D2 = 4, for a total of 19 damage. The standard Resistance soaks 2+D2 = 3 and the Fire Res of 2 soaks 1+D1 = 2, which results in a final 14 Fire Dmg - (3 + 2) = 9 Fire Damage. At the end, all damages are summed and applied to the target's hit points. Therefore, 19 standard damage + 9 Fire damge = 28 final damage.
The attack deals 20 standard damage and 8 radiation damage after Armour and Radiation Res have been applied. The target has 6 Fortitude and 3 Willpower. As a Scout class Templar, the Fortitude Class multiplier is 0.5 and the Willpower multiplier is 1.0. This results in 3 soak for toughness, 1+D2 rolls total of 2. And the Willpower soak is 3 as well, resulting in a 1+D2 rolls a total of 3. These are soaked out of the damage, and the true final damage is (20 - 3) + (8 - 3) = 22.
To assess how much damage is being dealt by both sides at any given experience level, open the combat log during a mission. It can be closed at any time after opening.
Negative Armor Bonus Damage
If you are able to lower a foe's armor down to a negative value (such as via the Scout's Piercing Fire), a special rule comes into play. Armor dropped below 0 points increases damage you deal to your foe at a rate of 1 damage per 2 points of negative armor. While extra damage is welcome, this makes excessive investment in armor subtracting debuffs not always the wisest use of your talent allocations.
However, if you are able to lower a foe's special armor, such as Fire Resistance, below 0 points, you gain bonus damage at a rate of 1 damage per 1 point of negative resistance (so long as your attack has a fire-based component.) This makes flame tank Engineers using Scorch Order before their default attack quite potent, especially in combination with Hydras. Another benefit of negative resistance is that the minimum damage your attack can deal is also increased, albeit at a rate of approximately 3 negative armor to 1 point of bonus damage. This is due to how all non-standard damage types work, always dealing at least 30% of maximum damage.
Related: Attack Gear Tactics