You can do some severe damage to the boss if you can save both your full-screen nuke and combine specials up until the end of the level. Use your nuke to quickly do some damage to the boss. Trigger your combine capability. You get a shield that makes you invincible for a couple of seconds when you are combined with your escort ships. Fly directly to in charge and fire at point blank range for optimum damage. This approach should truly make a damage in charge'health, if not straight-out ruin them!