Before the series begins the HPC was a primary method for ena removal. It is not specified who or what company developed the Cannon or made use of the Particles as a weapon. All Gardes are armed with them.
After Gauna 487's appearance, most of the Gardes make use of the cannon. Akai squad makes several successful strikes before their destruction. Nagate Tanikaze finally kills Gauna 487 with the use of the cannon and a Kabizashi.
While not applied much to the outer ena, the strike team made heavy use of their HPC's to clear their way to the host core on the LMU's interior. Sidonia used a massive version of the HPC to blast a massive hole in the LMU's front end, allowing the strike teams to enter.
The Heigus Particle Cannon utilizes Heigus Particle emitting crystals, a naturally occuring crystal used by Sidonia and the Gauna. The cannon sends electrical energy into the crystal causing it to emit a directional stream of high energy charged Heigus particles, which upon impact causes a Gauna's ena to evaporate away. The Garde's HPC is mounted on the mech's "head". A similar cannon is mounted on Sidonia's front end, so large and powerful that it blasted a massive hole in The massive Gauna structure's front.
The gauna are able to use their shapeshifting to recreate artificial Heigus Particle Cannons for use against the SIdonian Gardes. The effect on Gardes seems to vary, from light systems damage to overloading to complete destruction.
Gauna 487, after absorbing Eiko Yamano and defeating Akai squad, changed it's ena to make itself into an artifical Heigus Particle cannon. It's first shot was a close miss, but it was a enough miss to overload and shut down Norio Kunato's garde, as well as the rest of retrieval team. However, since the Tsugumori was less automated, it was able to overide this effect by rebooting.
Gauna 487's extra use of Heigus Particles also seemed to amplify Nagate's attack with his own cannon, causing 487's whole front end to be blown off, exposing it's ena.
Nobody knows how the Gauna can target the Gardes without technology. They may be able to follow the Heigus energy of the Gardes, or they may have some targeting method that no one has ever seen.
Once the strike teams began firing upon the surface of The massive Gauna structure, the whole Gauna pod suddenly created a deadly array of artificial cannons, blasting Gardes out of the sky. These "turrets" were each individual Gauna. How they too learned this method is unknown.
Since the Gauna use Heigus Particles for energy, using this weapon may strip off ena, but it also seems to increase the rate of ena regeneration.
The Gardes run on Heigus Particles, and firing the cannon drains the power reserves very quickly. When Sidonia fires it's Heigus Particle cannon, the whole ship experienced a blackout, as energy from every system was pumped into the cannon.