No Need for Introductions

I finally figured it out. I'm supposed to use the control switches to not fire the laser until the eye is open on the pyramid. I guess this allows the particle accelerator to charge up more to hurt the eye while it's open instead of wasting power shooting at it while it's closed.

I just had a really long pipe to store up the unwanted waste so my reactors would just keep pumping until the boss was beaten. The command centre took quite a bit of damage, but continuously firing and loading up with H202 got me through easily enough.

Another alternative is to allow the particle accelerator to fire continuously, but use the controls to hold back the hydrogen peroxide until the eye opens and then let it through to increase the voltage.