Natural Protection is Protection that a unit innately has, as opposed to Protection provided by Armor. It's the thickness of the unit's skin (or hide), or the toughness/hardness of whatever they're made of (if they're one of those golem things).

Items and armor generally don't modify Natural Protection. Magic can modify it, though, whether through changing the material composition of the character or providing a sort of enchantment. Here are some examples:

• Nature mages can turn a buddy's skin into tree bark (or something similar) with Barkskin. This provides a +7 boost, up to 10; if their Natural Protection is already 10 or higher, though, then the bonus is only a +1. This also provides -5 Fire Resistance.
• Earth mages can turn a buddy's skin into stone (or something similar) with Stoneskin. This provides a +10 boost, up to 15; if their Natural Protection is already 13 or higher, though, then the bonus is only a +3. This also provides -5 Cold Resistance.
• Earth mages could alternatively turn a buddy's skin into metal (or something similar) with Ironskin. This provides a +13 boost, up to 20; if their Natural Protection is already 16 or higher, though, then the bonus is only a +5. This also provides -5 Shock Resistance.
• Invulnerability from Stygian waters or other Death magic can substitute for Natural Protection, if it's higher. Magic damage slips right through this effect, however.

Note that none of these effects stack with each other. To see how Armor Protection and Natural Protection interact, click here.