Hi everyone, (mods if this is better in Official Fiction please move it)
I've not read all of the ED official fiction, but I've enjoyed AHTW so much I've now read it three times. The last time was mainly to help me try and fathom some of the things that were remaining mysterious to me, and it worked for some, but there are still many mysteries (or loose ends).
So I want to share these mysteries with you. WARNING, I've tried not to give away any of the storyline with these mysteries but there are probably still a few spoilers in there.
I've also included a list of things that are not in game as far as I can tell, and therefore are still mysteries for us as players. (also some things that are in game, plus some other things I thought were nice).
Enjoy!
Cheers 
I've not read all of the ED official fiction, but I've enjoyed AHTW so much I've now read it three times. The last time was mainly to help me try and fathom some of the things that were remaining mysterious to me, and it worked for some, but there are still many mysteries (or loose ends).
So I want to share these mysteries with you. WARNING, I've tried not to give away any of the storyline with these mysteries but there are probably still a few spoilers in there.
I've also included a list of things that are not in game as far as I can tell, and therefore are still mysteries for us as players. (also some things that are in game, plus some other things I thought were nice).
Enjoy!
General
Garry
Gunn
The Circle of Independent Elite Pilots
The Alliance
The Empire
The Federation
INRA
Thargoids
Other groups
Locations which are not yet in game (AFAIK)
From the new appendix so not canon:
Locations which are in game
References to things we should be able to do or use in-game, but currently can't
Noteworthy background "colour" stuff
- The second scene on the Behemoth confirms the FFE main storyline and that the Dark Wheel didn't find Raxxla.
Garry
- On New California why does use "Ryder" as a fake name? Is it random or subconciously?
- In the Ceeper base, why didn't Garry break his cuffs on the cell's plasma bars?
Gunn
- How come Gunn doesn't think Garry looks like Oberon?
- Where and how did Gunn try to commit suicide? Why was it very public? The Kum Bay Yar sect held hostages there, and in FFE they were based on Peter's Eden in the Arexack system. Are they still there?
- What happened on Thomson's World? How did Gunn's drink problem nearly ruin the peace process?
The Circle of Independent Elite Pilots
- Where was Oberon's coffin ship going?
- Oberon's black coffin had a bird-style crest on it, sounds like Elite symbol, with the Latin words underneath. What are the latin words?
- How did the Circle find them at Skardee IV after the misjump?
- What's going on with the architect, his grandson, the pink room and his daughter?
- What happened to the CIEP elders? Where did they go? Are they still out there?
- What about the other CIEP bases? There were between 4-7 because the project endure message went to seven people, four were base commanders. Are these other bases now abandoned, waiting to be found?
- What happened to Whithers and Gunn's other Ceeper "colleagues"?
The Alliance
- The Alliance helped stop a rebel imperial plot at Fort Donalds, Achenar. I believe that this is a nod to the FFE fan-fiction "Huge Plasma Accelerator" saga.
The Empire
- Was it definitely the hidden tracking device on Gunn's ship, put there by the Imperial clone agents, which led the Empire to the INRA mothership?
- Who was flying the Bismarck that attacked INRA?
- The next in line to the throne after Harald is called the "butcher" of Reorte, or "Saviour" by the Empire. Who is it? Denton Patreus?
The Federation
- What was FEDSOD operation Thunderstruck?
- Why didn't Blond and Brown double cross Garry and side with INRA? After all, the remaining INRA were all Federation, not Imperial.
INRA
- Does the Admiral know that Garry is really a Ceeper?
- Is crimson the uniform colour of INRA? Is this the uniform that also appears in Tales from the Frontier?
- Some INRA ships got away, where are they now? Are they still out there, regrouping?
Thargoids
- Is the green alloy that INRA Admiral McKowsky has from a thargoid ship? Meta-alloy?
Other groups
- Was the Calsace pirate gang from Calsace? I can't find that system, so maybe it's a family name.
- What involvement have the children of Raxxla? Why mention them in the new (note non-canon) appendix?
Locations which are not yet in game (AFAIK)
- Which system is Gunn's hidden circle space station in? It is probably a former imperial system since the rotation generates imperial standard gravity. It's somewhere explored, in the frontier, but apparently uninhabited apart from the Ceepers. The base is round a blue-white-green striped gas giant orbiting outside an asteroid belt around a red dwarf; it wasn't destroyed, so where is it?
- CD 32-331 system appears to be completely missing from game (in fact doesn't even appear in star catalogue). The Middleton gas giant is also missing.
- Garry base is at Hoopertown, but which system?
- The Garry clan raided a Wreaken Mining platform, the last place he saw his kilt! (until Varia Malin gave it back to him). Which system? Anything to do with the Wreaken from "Protest against Wreaken" or just chance?
- Arouca system, planet New Aberdeen, Granite City; planet Orkney, Kirkwall outpost. The system is there but the planets and stations are not - odd.
- Mariner Doldrums between Cemiess and Vequess, some sort of interstellar phenomena. What are these ?
- Achenar, Fort Donalds is where the alliance stopped a rebel imperial plot. Fort Donalds is missing… where would a space station go?!
- Has anyone seen the Thargoid war graves out past Leesti?
- Olcanze is where Robert and Jordan were prisoners once. Apparently some sort of Imperial mining location. Unfortunately it seems to be missing from the game.
- CD-73 253 system is there but the planet Tarlak is missing.
- Delta Phoenecis is there as well as the planets Anka, Kerkes and Garuda (the latter where they find the Imperial fleet), but planet Benu is missing.
- Smuggler 's junction is a pirate base hidden in an asteroid belt. The system apparently has two rogue planets and red dwarf star, but where is it?
- Aaymiay is mentioned in a song, is it a planet or a city?
From the new appendix so not canon:
- The Gibraltar's Run pirate den, not in game as far as I know.
- The Mastopolos Mining Incorporated strip mine is on Jennings Hollow in the Enayex System. The system exists but where is the planet?
Locations which are in game
- Skardee IV, the baking hot planet
- Leesti continental reef - but can't visit the reef yet!
- CIEP stole the Starburst weapon from Eta Cassiopeia… but which base?
- Brohman system, planet Villist, Tranquille Base - but can't land at Tranquille Base yet
- Tau Ceti coffee from Taylor's Landing - Taylor's Landing must be on the planet Taylor's Colony
- Morgue's Mortuary, planet in Eta Eta Cassiopeia where the Federation navy train
- Lanaest, where the CIEP tested the weapon on a gas platform
- Epsilon Eridani, New California, Masseyville, worldcraft corp, - can't land at Masseyville yet
- Cemiess
- Vequess, Agnews' Folly, where they first tried to stop the Ceepers
- Andceeth, lots of rich bankers there apparently
- Delta Pavonis, there's a ship dealer who sells Kraits there apparenently
- Grandmort, where the little statute is from
- HR 4790, where Jordan was once ambushed by the Federation
- Peter's Wreck in Facece, Imperial military and possibly prison world
References to things we should be able to do or use in-game, but currently can't
- The Lanner has a generation 3 hyperdrive which Sirius Corp couldn't make misjump; Garry did it by reactivating it just as they enter hyperspace, and NO manoeuvring. Is this possible in ED?
- The ability to over (or under) power modules - this would give more options for cool running, bravely-Sir-Robinning, etc.
- Sonic depth charges for bombing gas giants
- Riedquat ultra coffee - a rare good that's missing in game
- Starburst weapon, although to be honest it's a bit like an energy bomb, not exactly "balanced"!
- Eagle Explorer - is this just an Eagle fitted for exploration or a specific model? It is capitalised so assume a new model.
- Lakon Type IV freighter - in ED they start at type 6, so what happened to the type 4?
- Unidentified INRA ships, or are they just Condors?
- Imperial Bismarck battlecruiser
- Docking tubes used for large ships at space stations
- Federation Behemoth capital ship
- Liquid Inferno (a narcotic) - another potential rare good
- What is a "Carrack Killer" Asp?
Noteworthy background "colour" stuff
- Siloplastan acceleration couch
- Tollett and Marks, Vega Corp, Graves, Kenematic Armaments make weapons