I was doing the Paranid plot with the intention of combining the HOP and PAR factions into a single faction (TRI). I made it to the part where you build the station for them, but didn't want to complete it yet, as HOP controlled too much territory and it would make TRI span 1/2 of the galaxy.
At this point I got caught up other things I wanted to do, and was providing Argon ships from 4 shipyards and was building a 5th in Argon Prime, hoping they would push HOP back to their borders. As several hundred hours went by, HOP kept gaining ground vs ARG and had all but annihilated ANT. They had taken Second Contact II Flashpoint, Black Hole Sun IV, The Void, Antigone Memorial, Getsu Fune, and had multiple D stations in Argon Prime, which was down to just a shipyard and a few supporting stations.
It was when they started hitting the Shipyard in Argon Prime that I decided I had to get involved, so I strategically placed my fleets and went to war with HOP. After many hours of killing dozens of massive HOP fleets (Including many Odys that had nearly unkillable shields... literally, they kept recharging from 0 to full in about 3 seconds... No wonder they were doing so well... Only way to kill them was to target their shield gens with Disintegrators, which my Carriers' fighters were carrying 4 of), I annihilated their fleets and allowed ARG and ANT to reclaim their territories. I than took True Sight, Holy Vision, Cardina's Redress and Lasting Vengeance for myself, leaving only Pontifex's Claim in HOP's Hands.
I only let HOP keep PC because they had a TON of stations there and I expected I was going to be doing a LOOOONG series of criminal hunting to get myself out of the -29 rep hole I was going to have to dig my way out of to complete the Paranid Plot.
Rather than start with rebuilding rep, I decided to complete the plot station's construction, and amazing this allowed the plot to progress. On completion of the plot, All of HOP's remaining stations and ships swapped to TRI and I was now friendly with them. This left TRI with a very respectable 13 zones, rather than the 22 they would have had had I not knocked HOP out of power first.
TLDR: If HOP has taken over too much of the galaxy, you can advance the Paranid TRI plot to the point where you're building the station in Pious Mists II, than you can nearly wipe out HOP to prevent TRI from being a faction controlling 1/2 the galaxy.
