There are four aspects of gameplay in Phantom Dust: interaction, Arsenal building, mission assignment within the underground city, and combat in various arenas on the surface of the planet.
Within the underground city, the player can interact with other non-player characters to learn of missions, buy new skills, arrange and alter their Arsenals, and review memory boxes recovered during exploration. Once a player accepts a mission, they may have the opportunity to take a second friendly NPC to the field, though many times, the mission requires a specific NPC.
On a mission, the player and companion are put into a field with up to two enemy foes and the match begins. Each participant generally starts with 20 health points, but this may vary for weaker foes or stronger bosses. Due to the nature of the dust that fills each field, each match is limited to 15 minutes of game time, though if either all enemies are defeated, or the player's health drops to zero, or other special conditions are met, the match can end sooner.
Each participant will start with 4 random skills selected from their arsenal, and three orbs near their spawn point representing random skills with their color representing the type of skill, such as red for attack skills, blue for defensive skills, and white for Aura Particles. The player can learn what the spawned skill is by stepping over it, and subsequently can pick up by pressing one of the 4 colored buttons on the Xbox controller to assign it to that slot; any skill previously existing in that space is removed and lost for the rest of that match. After some delay, a new skill will replace one that has been picked up at the spawn point.
Skills typically require 1 or more Aura points to activate. The player starts with minimal Aura, but can increase their maximum capacity by collecting and using Aura Particles from their spawn point. When a skill is used, the aura is temporarily drained from the player but will recover slowly up to the maximum capacity. Skills themselves fall into 5 Schools describing the type of damage or effect they do, the amount of damage that they deal or protect against. There are 6 types of skills available in the game:
- Attack skills perform direct damage against the opponent. These skill have a strength value (STR) from 1 to 10 or X amount, a range, and a trajectory or attack type (such as direct shots, falling from the sky, striking in an arc, or sliced like a sword blade). Attack are not guaranteed hits; if the opponent moves to the appropriate type of cover, uses a defensive skill, moves out of range of the attack, or simply moves out of its way, the attack will fail to hit.
- Defense skills protect the player by certain means, sometimes limited to attacks from skills in specific classes.
- Status skills can alter the statistics of a combatant, such as increasing or decreasing attack power.
- Erase skills can remove loaded skills from other players or from players spawn points.
- Special skills typically allow the combatant to alter the playfield somehow, such as by flying, teleporting, or changing spawn points for new skills.
- Environmental skills affect all combatants directly, generally restricting certain actions, such duplicating Aura regeneration speed or disallow skills that deal >3 damage, until someone removes the Environmental Crystal from the playfield.
Skills are generally one-shot; once the skill is used, it is removed from the combatant's loaded skills and lost for the rest of the match. However, some skills have two or more uses and other skills can be used indefinitely.
When an opponent takes damage, they are given a few seconds of invulnerability (indicated by a translucent appearance) which they cannot be damaged.
While manipulating and using skills, the combatants can freely move across the highly-destructible field. A player can rotate the camera as needed though they can also lock on to an enemy combat or ally as well. It is quite possible for a combatant to fall out of a field, such as falling through a destroyed floor or knocked off a ledge; the combatant will reenter battle at their respective spawn point but with a loss of 3 life points.
