The combat in 99 Spirits is turn-based.
Choose the Attack or Defend command to fight.

Attacking and Defending

Attack You attack several times in succession. You can execute more attacks with the help of certain Tsukumogami.

Defend You block several times in a row. You increase the corresponding Gem Gauges by attacking or defending.

Enemy Turn

Between your attacks or defense, the enemy will randomly attack you.
When that happens, Defend (key X) and Counter (key Z) to block and counter-attack the enemy.

If your Defense fails here, you will take damage.
Be sure to defend well to control the flow of the battle.