In Phase 2, the Flagship gains a powerful Drone Surge ability, launching a swarm of combat and defense drones. It also retains its main weapons. Your strategy here should focus on dealing with the drones while continuing to damage the ship. An Anti-Drone Drone or a strong Defense Drone can help. If you have a teleporter, boarding the Drone Control room can shut down the surge. Be prepared for hull breaches and fires.

- Target Priority: Drone Control (if boarding) > Missile Launcher > Shields.
- Defense: Defense Drones are highly recommended.
- Offense: Maintain pressure on shields and weapons.
- Special: Prepare for drone swarms and potential hull breaches.