When performing Thunder Shoot, the Fly Type member on the team punts one of the team members currently holding onto him/her forward, like kicking a ball. In the process, the launched team member is conferred in a crackling shield of electricity. Once the launched team member hits an enemy, the enemy in question will become temporarily stunned and as well take damage if the Thunder Shoot is powerful enough, while the launched teammate returns to his/her position in the team formation. Armored enemies are immune to damage from this move however.
To perform Thunder Shoot in gameplay, the selected team must be in Fly Formation and have at least one other team member present or the move will fail. The player then has to press the Attack button (//) to launch the teammates at enemies. When launched away, the teammate will home onto any nearby target. When used on airborne enemies, the move will cause them to drop to the ground. For as long as the player has other team members present, the player can continue to use Thunder Shoot in succession.
Aside from attacking enemies, the player can also use Thunder Shoot to trigger Target Switches in the air, strike hovering metallic containers down to the ground, or fill the Team Blast Gauge (although it fills a very partial amount).
By collecting yellow Power Cores during gameplay, the player can increase the power, effect and radius of the Thunder Shoot. The levels of power are as follows:
Level 0: Thunder will only stun enemies and the target will recover from the stun after a short time. It can only hit one target. Shot team member will receive damage when the attack connects.
Level 1: Thunder Shoot will damage the target by one hit point and stun the target for a slightly longer time. It can possibly hit two targets during one shot.
Level 2: Thunder Shoot has a slight chance of destroying the target. If not destroyed, the stun effect will last a long time. It can hit multiple targets.
Level 3: Thunder Shoot inflicts heavy damage on target and inflicts stun. It can hit all targets within shooting range and draws in nearby Rings.