Right, so. Despite certain claims that I have been kidnapped and devoured by a dingo in serious need of a diagram explaining what a baby is and isn't, I am in fact alive. I'm just not writing for anymore. It is no longer relevant to my interests. You might find me on Spacebattles or Fimfiction, but this story won't be appearing in either place.
As you might imagine, this means that the story is for all intents and purposes dead. Sorry guys: shit happens.
But someone asked if I could give a breakdown of what I had planned for later chapters, which I thought was a perfectly reasonable request. Even after so long, I got a general idea of where I wanted to go with things. I can't break the ideas down to specific chapters or character interactions, but I can give a brief overview of what each planet/character arc would look like.
The Therum Arc
In the last chapter, the Shades made their appearance properly. Their purpose in attacking the colony was to secure the Fourth Gen InVitros for their own purposes, the leader of the group offering Shepard a choice: let them take the children, and the Shades would fight Benezia and her commandos while Shepard spirited Liara away. Shepard would agree, reasoning to himself that at least with the Shades the children would at least maybe be raise to be something other than disposable assets. Shep and Liara would attempt to flee, only to be pursued by Benezia, who would keep her weird fascination with motherhood going. Just as in canon, she'd get her ass killed in the first enounter. Unlike in canon, I wanted her end to be a lot sadder. Turns out her fixation on motherhood is actually the only thing she really has left due to the Indoctrination process, and that specific fixation was Liara was the most important thing in the world to her. She even reveals that Liara doesn't really know any critical information: Benezia was just hung up on trying to keep her daughter safe. Shep & co. leave the planet, but Liara is devestated that she had a hand in killing her own mother. Shepard is worried, because he convinced her to do it.
The conclusion of this mission: Shep learns about Indoctrination and it's effects. Sad Liara is sad.
The Feros Arc
Feros is being besieged by the Geth and Saren, and Exogeni calls on the CEG Rapid Response department (a branch of the CEG military made available to the corporations and Fringe Worlds for the purpose of defense... for a price,) as well as the Citadel for help. When Shepard arrives, he finds Kaidan already there, organizing the local militia to better defend the colony. Kaidan agrees to help Shepard launch an assault against the Exogeni research facility, if only because he has a major hate-boner for Turians and wants to turn Saren's mandibles into a back-scratcher. The assault would reveal that Exogeni was studying the Thorian just as in canon, but a damn sight more sensibly. The Thorian's telepathy and extreme longevity are researched in depth, the former especially as it seems to be compatible with humans on some level. Unlike in canon, Saren isn't looking for information on the conduit: he's trying to destroy the entire colony to make sure Exogeni's research never sees the light of day. Shep and crew would fight a three-way battle against both Saren and the Thorian, who is understandably pissed off about being reduced to a lab rat for decades and proceeds to mind fuck the entire colony... except for Shep, who proceeds to wreck shit like it's his job. Saren is injured, but escapes. The Thorian has it's shit wrecked. Shepard finds that while he was busy fighting Saren the Geth were actually being competent and destroyed the Exogeni information structure and killed all researchers involved. Shepard is forced to move on, and Kaidan comes with him for unexplained reasons. Shepard is worried by what his apparent immunity to the Thorian's influences might imply.
The conclusion to draw from this: the Triumvirate of Evil are very interested in telepathy. Scary Kaidan is scary.
Noveria Arc
This arc sees the return of Ashley, as she takes the place of Giana, that one woman who wants to arrest the colony administrator. Shepard would receive information from his previous employers, the Turing Oversight Committee. They would tell him that Citizen Kane was currently assaulting a Soul Market research facility on Noveria, and that it would be a good idea for everyone if Shep were to wreck shit like a wrecking ball. Ash is more than happy to help Shepard gain access to the Soul Market base so long as he brings her along with him. Shep & co. assault the base, and quickly discovers that the base is actually the residence of Citizen Charon, the majority shareholder of the Soul Market and a Complete Monster. Charon is revealed to having developed a method to "eat" SOULs, absorbing and incorporating the memories, skills and personalities contained within them into his own being. Charon has been having people forcefully implanted and then held captive for the express purpose of one day killing them and then devouring their SOUL in an attempt to grow a soul (in the spiritual sense) of his own. Because he is crazy. Kane is there to learn how Charon does his creepy party trick by any means necessary. Shepard understandably decides that the best solution to the problem is to destroy the entire facility with extreme prejudice, and Ashley reveals her where her true loyalties lie: the Soul Market. She's trying to work up enough money to purchase her parent's SOULs and have them reimplanted, and on Charon's orders betrays Shepard again. She eventually turns on Charon, realizing that Kane and Saren are more important than her parents... for now. The facility gets destroyed, but not before Kane manages to transmit himself offplanet with a fancy new trick up his sleeve. Shep is worried because he managed to turn a traitorous wench like Ash into a loyal friend...
The conclusion to draw from this: Kane isn't affected by Indoctrination... and he's looking for a way to incorporate new code into his own. Complicated Ashley is complicated.
Virmire Arc
Not much changes from the canon except the revelations from Sovereign. Instead of simply saying "you die because we say you do", he actually explains why the Reapers keep coming back every so often: they're trying to prevent the total extinction of complex biological life, because races keep evolving telepathic abilities they don't know how to use and then proceed to cause a galactic scale extinction event through a variety of ways: the emergence of Arda Yakshi-like races that melt brains, psychic domination/indoctrination on a galactic scale, cataclysmic empathic feedback on a galactic scale that kills civilization through depression... the Reapers have seen a lot of ways for biological life to fail at living, and the waste of it all disturbs them. Kane and Saren are revealed to be looking for ways to either prevent or circumvent a possible mass extinction event, (Saren seeks to suppress or eliminate psychic abilities completely, Kane wants to turn all organize sentient life into synthetics so they can never be wiped out by such an extinction event,) but Sovereign says that they're too late: the foundation of the apocalypse is already set, because Shepard already possesses formidable telepathic abilities. And if an InVitro has them, then it's possible and indeed likely that the others would as well. Sovereign takes off for Ilos, and Shep leaves either Kaidan or Ashley to die with Saren. (Since Saren's already too late for his own plan to become reality, he volunteers to try and hold Shep & co. for as long as possible while Sovereign and Kane try to fix things.)
Ilos Arc
Nothing too different here. Shep learns that the Protheans actually won the war against the Reapers, only for the abilities of the true Prothean (the ones with the psychometry) to develop into all out domination-auras that completely enslaved all those around a sufficiently powerful mind. Vigil explains that their civilization crumbled as powerful warlords vied for total domination of the galaxy and slowly went batshit crazy with greed.
Citadel Arc
Final confrontation with Kane, and Shepard breaks down Kane's resolve in typical Paragon fashion by pointing out that even if Kane succeeds he'll still be destroying the lives of trillions of people at best and annihilating civilizations at worst, and that the Reapers might not even be right about the supposed psychic apocalypse. Kane, turning out to actually be kind of a decent person despite fully endorsing the Zeroth Law of robotics and everything it entails, decides to turn Charon's ability to try and eat Sovereign. He fails, and his code becomes incorporated by Sov. Shep and Sov (in the body of Kane) fight, and Shep gets his ass handed to him. Because psychic ninja cyborg clone does not trump psychic zombie terminator. Sov is about to open the Citadel up for the rest of the Reapers, but a fragment of Kane's consciousness transmits a codeword that can be used to force a self-termination sequence. (It's "Rosebud".) This stuns Sov long enough for Citadel forces to rally and destroy the Reaper, and the day is won. Tali and Shepard ride off into the sunset on a lion, and have much sex.
Character Backgrounds/Arcs
Kaidan
Key difference from canon: instead of killing Vyrnnus in BAaT, Kaidan got his ass beat by the Turian. He then proceeded to kill Raida in a rage, and then the whole program got shut down. Kaidan hates Turians with the fury of a thousand suns, and joined the Rapid Response section specifically for the chance to fight them. I wanted for him and Garrus to bond over their mutual hatred for bureaucracy and Turian criminal scum as well as vigilantism. To become the Red Hood to Garrus' Batman, if you will. (That's about as close as I can get the comparison, I think.)
Ashley
Key difference from canon: her father was a colonial administrator for Chimera Labs, and when the company was blacklisted and their assets seized by the CEG he and his wife were killed trying to save their children from the skirmish. Ashley grew up having to support her sisters, and became a corporate samurai at first out of necessity and then out of hatred for the CEG. Charon acquired her loyalty when he revealed that he had procured her parent's Souls, and gave them to her with the promise that he would grow them new bodies provided she agreed to serve as one of his agents and retainers. I wanted to have her appear as someone intensely selfish, only for her to have to give up her own desires at the culmination of the Noveria mission for the good of... well, whatever Shepard made her want. It's supposed to be both nice and horrifying in retrospect. She's very proud of being able to provide a safe life for her sisters, and will end anyone who endangers them.
Shepard
Look at the above sentence. Yeah, that's his primary conflict: that he's part of the reason why things are going to hell in a handbasket, and that he ultimately has no idea how to resolve that problem any further than trying really hard not to end all life in the galaxy.
Tali/Shepard
... strangely, this is the part that I remember the least about. I know I wanted the two to bond over their mutual interest in synthetic life, and for Tali to have awkward "humans are weird" moments and for Shepard to get very uncomfortable with technically being a synthetic life form himself. I wanted them to be awkward together, because flustered Tali is too cute to handle.
Liara
Liara was supposed to really be messed up by the death of her mother. Y'know, like you'd be if you willingly became a matricide. And then I wanted her to lose her fucking shit when she realized that Shepard might and forced her to do it on Virmire. Wasn't too certain where I wanted to go with that.
Wrex
I wanted him to be kinda of nonchalant about everything. I wanted him to be okay with the end of the galaxy, because as far as he was concerned it was over anyway because his people were going to die anyways. And then I wanted Shepard to maybe/somehow give him some hope, and actually want to turn things around for the Krogans.