Players control Zak, an amnesiac who wakes up on the island of Gipath and is quickly dubbed the Chosen One by the local villagers, mostly as a way of tricking him into solving their problems for them. He must discover his lost memories as well as helping various NPCs and factions to progress further across the island. As the game continues, Zak is able to explore other lands beyond Gipath.
He can be accompanied by up to two followers who are controlled by the player as well. The player must manage their tactics in battle separately, even sending them off to perform independent tasks, in much the same way as the Infinity Engine games.
Each character has a health bar, with death occurring should the bar ever empty. They also have a stamina bar, which goes down whenever the character runs or uses magic. If the character stands still, the stamina bar will quickly fill up. Therefore, healing back to full in non-combat situations is relatively easy, though stamina is a constant concern mid-battle as it does not refill if the character is in combat.
Most of the game's action takes place in "game-zones", which are 3D landscape "maps" that the player explores to fulfill quests he is given by various NPCs. Usually, exploring beyond quest areas means encountering enemies and situations beyond one's current ability, though a stealthy character might find a way around. Enemies do not respawn once killed in an area, so it's often in the player's best interest to "genocide" the level-appropriate creatures in any given area for maximum XP gain and item drops.
There are many situations where the player cannot blindly charge into a fight and must use the stealth system. Characters have four modes of mobility: Run (which is quick but uses stamina), Walk (default), Crouch (slow, but harder to spot), Crawl (slowest, but hardest to spot). A few special enemies are designed to be far too powerful to fight and need to be snuck by.
The game has a diverse crafting system, which allows the player to take apart weapons and armor Zak finds and reconstruct them with stronger materials and magic. Materials can be readily found on most enemies (as well as regular vendor trash with no other purpose than to sell). However, crafting is only available in stores, and the player's inventory and level-up screens are only accessible in stores and on the world map between areas. Players must make sure they have all the right equipment on before entering a game-zone.
Characters level up based on XP they are constantly accruing. Half of this XP is automatically transferred into bonus HP and Magic, and thus isn't accessible to the player. The other half can be assigned to six classes: Melee (close combat), Archery (ranged combat), Use/Steal (the ability to use items and steal from enemies when in-stealth), Elemental Magic (mostly attack, some buffs), Astral Magic (healing, buffs and debuffs) and Sensory Magic (mostly buffs concerning scouting/divination). Characters can also choose specializations in weapons and magic, as well as stat boosts, faster stamina or health regeneration, encumbrance (which decides how much heavy armor the character can wear), nightvision and more. As a character picks up more specializations, remaining ones become more expensive to "buy" with XP, forcing the player to be selective when choosing the most appropriate skills for that character.
Though the player is able to level-up and equip companions, Zak must abandon them each time he leaves an island for the next. There are plenty to choose from on each of the three islands, most with pre-set specializations. Which two to take is up to the player's discretion, how they've chosen to build Zak and their own play-style.