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!
Several mods are known to cause some problems with this plotline. All mods not updated for 2.6 are suspect and even if they have there's still no guarantee that they're compatible. If you have a plotline problem with a modded game, you are requested to go to S&M and ask which mods might be the culprit, and then ask in that mod's forum thread for possible solutions.
This plotline is characterised by long strings of triggers, and it has been found by experiment that sections of this Plot are quite unstable and prone to failing in ways which (presently) remain unexplained. Although everything will probably be fine, it is suggested that you save often and under different save files whilst conducting plot related missions.
Thanks to all those who have contributed below. We now begin.
Chapter 1; Freedom's Reach
The plot begins when you are between 2 and 6 sectors away from Danna's Chance, after you've completed the Terran and Goner plots. You'll get a message to respond to.
You can tell them that you're busy; the mission will disappear for 30 minutes and will reappear the next time you get within the right range of Danna's Chance. However as of 2.6, it seems that if you do this, then every time the plot start message is triggered the game will duplicate all of the plot critical ships that it adds at the start. It is recommended by myself that you accept the first time and complete the first mission; it is not hard or particularly time consuming if you have more than 5 million Credits and will leave you at a point where you can forget about it indefinitely without being bothered by a message every 30 minutes.
I believe that as of V3.0, the repeated spawns problem has been rectified.
Anyway, to the message;
The CPU ship is now blocking the gate on the other side. If you try to jump through to Freedom's Reach using the sector gates, you WILL die, whether you fly through the South gate of Danna's Chance or use your jumpdrive. You can't even use escorts, as they'll be automatically blown to bits by the CPU ship's influence. You have to use the UFJD to get past, beginning anywhere other than Freedom's Reach...
The station is under attack by a few fighters but unless you're flying an Aran then you'll get there in plenty of time to save it, especially since the station is invulnerable. The tricky bit is getting there before there are too many fighters for you to deal with. I did it in a Chokaro, and didn't even need to launch the fighters I had docked. It is possible (if you leave the TM out of range) to take a docked fighter and blow the attacking fighters up that way, but as more fighters will arrive from the CPU ship in time, speed is of the essence and the Chokaro has enough killing power to take down the fighters, as do several other popular TMs. Stay with the station, don't go chasing off after the cloud of fighters surrounding the CPU ship, you don't get points for blowing those to bits. Keep your reticle on the eight or so fighters swarming the station for a quick conclusion to the mission.
Be very wary of accidentally hitting the station with your turret fire. It's game over if you do. The missiles that you were instructed to bring can be used to pick off the attacking fighters without accidentally landing PAC fire on the Trading Station.
Repeated bug here; If you have a large complex or presence in Freedom's Reach before beginning the mission, then collision avoidance algorithms can dump the CPU ship right on top of the Trading Station. If this happens, reload and hope it finds somewhere different the next time you jump in.
Once you've destroyed three of the attacking fighters, and after a time limit, you'll get a message to dock with the station. If you're flying a fighter around, then DON'T just call in the TM. The CPU ship is transmitting some sort of virus on the comm bands that causes ship systems to fail; any ship not player-piloted will blow up if it gets too close to the CPU ship. You have to fly back out of range and transfer to the TM by docking. When you are ready to dock with the station, make sure that you have enough cargo space for the 100-odd passengers, as it seems that glitches can (but not always do) occur if you don't. You need almost 600 cargo units worth; you'll get the civvies transferred (and you'll be given a free CLS if you didn't already have one) and then you just need to jump back to Elena's Fortune using standard jump and dock at the Military Outpost. As of later varsions it will give you the Energy Cells if you don't have enough. Section complete.
Second common bug; The passengers do not always appear in the cargo list. Nevertheless, if the mission guidance points you to Elena's Fortune, go there and the mission should complete successfully.
Now dump that TM and get in something quick.
You can break from the plot here if you like, and come back to it later.
We're looking for a Boron scientist, Bola Hi, who is in Queen's Retribution. He's supposed to be on the shipyard, but when you get there, he's out on a research mission in the Aldrin system. So begins the long hunt.
When you get to Aldrin, you need to make your way right round the rock to the correct Aldrin station (whichever one has the book symbol; it's random). The Trans-Orbital Accelerators make things quicker. A Kestrel makes things even quicker still, but it helps if the thing has a jumpdrive and a couple of E-cells as you'll be going all around this blasted asteroid.
When you get to the Ship Production Base, the chief engineer has never even HEARD of the Boron. He directs you back to the Unknown Base right next to the TOA by which you entered the sector...
When you get here, dock, and you'll be able to talk to the USC professor Ketraar, who puts you in contact with the Boron scientist. After a short wait, you get another message telling you that they've decoded enough of the message to send you on your way again...
Oh, wonderful. MORE UFJD jumps. At the rate I'm going, my Hyperion won't have any systems left by the time I find this thing we're looking for... Particularly since it takes several Jumps to find the right sector. Just keep going until you get there, you will get there eventually and you'll know it when you do.
You'll need a Cargo Lifesupport System before you continue.
You can break from the plot before starting this, as the next bit isn't initiated until you start using the UFJD. Just remember that if you do want to use the UFJD for something, you're going to initiate the plotline again...
Keep UFJDing until you get a message telling you your jumpdrive just failed (deja-vu here... ... last guy who this happened to ended up... WAIT A MINUTE!!!!??? ). You're now in the right sector. Rather permanently, it seems. You cruise to some ship debris indicated by your HUD and from there, #efaa appears. Go up to her, and she decides that you're hostile. Your ship computer will briefly malfunction. After some convincing (the bottom of the two responses is the one you want), #efaa accepts that you mean no harm and demands control of your ship computer...
Ordinarily, I'm not that stupid. But, it doesn't seem that we've got much of a choice, do we? There's an 8 minute wait whilst #efaa accesses your ship computer and reconfigures your jumpdrive.
#efaa takes us back to Freedom's Reach, and tells us to fly up to #cafe. We have to break #cafe's firewall, and to do that requires codebreaking!
We also get an annonymous message from what appears to be a Martin Winters wannabe...
First, you've got to break a 4-digit code. It isn't too hard, as it tells you how many of the 4 digits are right (green), wrong (red), and in the wrong place (yellow). Problem is, it changes if you take too many tries or abort the attempt. You've got quite a few though, I've taken 11 in one attempt without being booted out. Here (link) is Roger L.S. Griffiths' contribution to helping you solve this one.
Next there's a Sudoku puzzle to solve... or get a sudoku solver to do for you! Inputting the data takes bloody ages, take your time and make sure that you get it right! If you don't have a window (seems to be a common bug), make sure that you're in comms range and then comm the #cafe. If that doesn't work, fly away from it and approach again.
Stage 3 involves putting a password into the mainframe. The password is #cafe's code then #efaa's code appended; USCWintersalpha_omegaUSCMarteen_earth_plus.omega
#efaa gives you her code, you get #cafe's from the garbled messages that you'd recieved when she was malfunctioning in chapter 1. Another bug here, particularly in non-English language versions, is that the correct password sometimes does not compute correctly for a reason not presently determined. Check that you've got it correct, as X does not take kindly to double letters in input strings so you might be missing the odd letter.
With this, #cafe stops its murderous rampage and it's time for a new mission. Get ready...
There, you pick up the Teladi station owner and have to taxi him back to Freedom's Reach, where he discusses your payment... Don't read the next spoiler if you don't want to know what it is.
Once you've paid up, your sector is spawned; it's north of the Unknown Sector that is east of Zyarth's Dominion. You get to choose its name from a list, and that determines some of the sector aesthetics as well as what resources are available (it's roughly the same for each Sector though, <see link>, so it doesn't really matter). It has 'roids and it's off the beaten path; good for building a factory complex.