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Cloaking helps immensely. You could take defense drones and healing drones, but maxed engines plus cloaking is my preferred method of dealing with Phase 2 with minimal damage.

Since the primary weapon arrays are self-contained, killing the operators will prevent repair. They repair but don't re-man each phase. Deal with the missiles, then the ions, then the blasters, then the lasers. Without weapons, the ship's much easier to beat.