This walkthrough is mostly spoilered, so that if people get caught on the common sticking-points they can read it without spoiling the story for themselves.
However, it is not expected that the replies will be spoilered, so don't read beyond the first post if you are stuck but don't want to know the plot!
As one of the original plotlines, only very early versions of the game have appreciable bugs. However, if you have mods, it is possible that they may introduce problems with the plot. As this is a Vanilla forum and a repository for information and issues regarding the unmodded game, if you have a problem with a modded game you are requested to post in the Scripts and Modding forum.
The HQ plot begins 6 hours after the HUB plot is completed. You will get a message from a Boron named Humi Wi asking you to report to Ocean of Fantasy. This indicates that the plot is available to start.
You will need a squad of experienced Marines to successfully conclude this plot.
When you arrive, your contact will be aboard a Boron Ray in the sector. Chat to him to start the plot.
Chapter 1; Summoned.
You arrive just in time to watch the lab get blown to bits. There’s quite a hefty Yaki fighter force causing havoc, but given the amount of combat you’ll have seen by now you should be able to handle it. Just beware of Plasma Burst Generators, and some of the Raijins may have Pulsed Beam Emitters.
When the Yaki are dust, report back to the Ray in Ocean of Fantasy. When you get within range, you get your next mission.
Jump to the sector. It’s possible that you might be able to pick up a couple of Enhanced ships here that are otherwise unavailable, if you find one then save and cap it. If you don’t, reload until you do. Unless you don’t care, in which case, you’ll find a Military Outpost by the South gate; that can only be bad news. Fly in close, then report it back to Tomas Brano in Cloudbase Southwest when instructed.
After that, the fleet jumps in and engages the Yaki. You have to destroy the station without much help; the AI is too dumb to employ firing patterns that are effective against stations. If you want to avoid losing Yaki rep, then take two ships; one with a load of heavy torpedoes, and one escort. The no-rep-loss missile trick works by firing enough missiles to annihilate the target from one ship, transferring to another ship and then jumping the original ship out before its missiles strike the target.
You are recalled to Kingdom End on completion of the mission.
Say hi to Mahi Ma again. He briefs you on the scientists; they’re being held in Olmanketslat’s Treaty. They can get to a ship but they can’t leave the sector without cover. You’ll provide that cover, along with a small Boron strike force, but that won’t arrive until later.
When you get close to the base, which is usually located close to one of the Gates in that sector, the Boron are already making their getaway. Take out the pursuers. The strike force will be jumping in and moving to engage but they’re too slow to be of any use. It’s possible that they’ll move in the wrong direction entirely.
Saving the Boron scientists shouldn’t be too much trouble. One or two may not make it but you have to lose a good many to fail the mission. Once they’ve all got to the Gate, you get a recall order in Kingdom End.
When you find the Orca and your Marines are in sector, the Orca turns red (if yours doesn't, check the registration against the one given; you might be about to send Hell's Fury after a perfectly innocent supply transporter). It has indeed been captured by the Yaki. This is a simple boarding operation; the Orca has no escorts, but it will try to shoot down incoming pods. You are best launching at least a few swarm missiles as cover; you can’t destroy the ship as it’s invincible until you capture it. When your Marines are aboard, they should be able to fight their way through the ship, assuming their level is high enough.