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The Phase Pulse Generators are devices built by the Forerunners into their Halo installations. Halo's main weapon is powered by three phase pulse generators. They amplify Halo's signal, and allow it to fire deep into space. The power levels are massive. How they produce such prodigious amounts of energy is unknown. The generators could possibly emit a gamma ray burst. They are susceptible to close range EMP (Electromagnetic Pulse) discharges, and destabilize if they come in contact with an EMP.
Cortana had John-117 disable these while on the first Halo, in order to delay the Installation's activation so they would have time to destroy it, and to prevent 343 Guilty Spark from "Finding another way of activating Halo." They accomplished this by turning the Shield Generators from the Mark V armour he was wearing into a crude yet effective EMP bomb, that once activated knocked out the Master Chief's shielding for a short time.
It is not known where the Phase Pulse Generators are. It is possible that unlike Alpha Halo, it uses only one large generator, within the Control Room itself. This might be a shield generator for Halo, or it may serve as a power source for Halo. However, during the fight with Tartaraus, 343 Guilty Spark says that the "primary generators are coming online."
Installation 04 (B)Edit
Two of the pulse generators can be found on the last level of Halo 3, Halo. Unlike the other generators in the first Installation 04, these can't be destroyed and seem to be more protected, an example of this is that the glass in the room surrounding them is unbreakable and some more barriers have been placed in the perimeter.
These generators also seem to be weaker, as they don't have a continuous beam. The reason for that may be that the Halo wasn't completed at the time. These generators were likely destroyed in the resulting chaos of the Installation's firing sequence, this could explain why John-117 was not killed by the energy pulse seen racing past him in the cutscene at the end of the level.