A second version of G-Darius was released in the arcades in 1999, with the following changes:
- Increased difficulty.
- Default play cost is increased to 2 coins per credit from 1 coin per credit.
- Added Beginner Mode; in this mode, the game ends after completing only 3 zones.
- Standard auto-fire button.
- When using a Capture Ball, the player is no longer invulnerable.
- With the super shield, the player is vulnerable to obstacles; with the hyper shield, the player can take a single hit from obstacles.
- All stages include mid-bosses; moreover, they all fire the spiral laser from First Captain at the player.
- Boss battles include a timer - three minutes for normal bosses, seven minutes for the final boss - with 10000 bonus points added to the player's score for each remaining second upon destroying the boss.
- The high score table records high scores for each zone.
- After continuing, the player is given one of each Missile, Bomb, Arm and Capture Ball power-ups, instead of a single item that provides the first three.
