Authors Notes: This one covers the two years between Mass Effect and Mass Effect 2. (The first covered in MD1 and MD2, and the latter is covered in MD4). The timeline elements from the outline has been removed as it was purely for me on a writing standpoint. Beware, there are parts that will spoil the story for you in places. But since I doubt I'd ever get to actually write this story to how I want, that's why I'm posting the outlines.
Chapter 1 - The Siege of the Citadel
The Battle of the Citadel continues within the Citadel, Fighting Geth ground forces.
Chapter 2 - To the Four Winds
Squad members leaving the Normandy.
Chapter 3 - Operations Officer Mcpherson
Change of Identity for Stephen, to Alex, Training in Arcturus. Tali is granted permission for sharing the Tantalus Drive Core tech.
Chapter 4 - Hunting Geth
On the Normandy, Jennifer Shepard and the crew of the Normandy struggle in their fight to drive the Geth back to the Perseus Veil without the assistance of Shepard's squad.
Chapter 5 - Sabotage in Argos Rho
Alex has completed part of his Tier-3 training, and is taking leave with Tali to begin work in the Argos Rho Cluster, and gains a bit of help from Shepard while her new ground squad are on Pinnacle Station, training.
Chapter 6 - Quarian Flotilla
Alex and Tali are onboard the Normandy, as Tali is finally returning home. Shepard is unable to stay, however, but Alex has access to a FTL-capable shuttle so he can leave when he needs to. Alex is present at Tali's, 'inauguration' into the crew of the Neema.
Chapter 7 - Investigation and Delayed Bad News
Part 1
Alex is transferred to the embassy on the Citadel, to await word on his first posting from Captain – now Councillor, Anderson. During his wait, he begins his investigations into the Collectors, using evidence discovered during the mission to stop Saren. Partway through, however, he hears about the Normandy.
Chapter 8 - Investigation and Delayed Bad News
Part 2
Alex joins up with a rather matured Liara T'Soni, and the pair begin tracking down Shepard's body. They discover that the Shadow Broker recovered Shepard, and is intending to sell her body to the Collectors. Distraught that she did indeed die from spacing, the pair fights tooth and nail to stop the deal and recover the body.
Chapter 9 - Death Won't Be The End
They have recovered Shepard's body from the Shadow Broker, but that is only the start of the issue, as several wrenches are thrown into the works, one of which Alex recognises. Eventually, even they admit they cannot protect Shepard from the collectors, and only a face rather familiar will be able to, and more.
Chapter 10 - Cerberus
While Liara observes the transfer of Shepard's Body to a Cerberus transport, Alex ensures that he can monitor Lazarus Cell, going so far as to plant a tracer of his and Tali's own devising onto the ship, and pulls, 'An Obi-wan from Attack of the Clones'.
Chapter 11 - Breakthrough
Having long ago hired the services of a Salarian research team, Alex hears back in regards to duplicating the Quantum Synapse technology, essentially an advancement of the 'Blue Box' technology that allows truly sapient Artificial Intelligence. Concurrently, the efforts in Argos Rho succeed in rendering it a deserted Cluster, and so the process of stripping the abandoned Pinnacle Station and installation of a new sub-orbital station within Sylsalto, a large Ice-Gas Giant. Also, one last piece of luck brings Alex one step closer to his personal goal of creating a Sapient AI.
Chapter 12 - Arcs of Angels
Alex' life has been busy for a long time, as he has many things running at once. Investigating the Collectors, building up his resources, building up his skills, and working on 'Project Derevko'. And only when he receives a cryptic message, is he brought out of the stressful triple-life and fully into getting back in touch with his friends.
Chapter 13 - Bout Damn Time
The Funeral for Shepard is only days away, and the crew are back. To keep his cover, Alex pretends to have met Stephen, when he was introduced to Tali on Arcturus Station. The Squad are brought in on his Identity change and that it was actually Shepard's idea, since 'bringing someone back from the dead was a bigger nightmare of paperwork'. Finally, time comes for the Funeral. He's surprised to see Another headstone, it's a double Funeral. "Stephen *********"
Chapter 14 - Set-Backs
His Salarian teams have finished creating the technology that would, automatically, produce 'Quantum Synaptic Processors', and only luck has the technology already in Argos Rho, with a fake shipment going elsewhere, when the research station is invaded and most of the team die in defence of the labs. Alex is on another off-the-books visit, and manages to only save 2 of the Salarians. Well away from the station, he activates hidden detonators, destroying most of the structure keeping the station together, and turns its own defences onto itself. Alex swears to fire back.
Chapter 15 - Strike-Back
Alex is infiltrating a Cerberus outpost, and finds the location of the Cell's databanks. It's a cell dedicated to AI research, including the 'EDI' project. He wants it, and he won't stop at anything to get it.
Chapter 16 - Project Derevko
Returning from the mission to Intai'sei, Alex has begun modifying the EDI program, and has enlisted the help of Tali and the two Salarians, whom are brought into the plan, and told what he was aiming for,, and how it actually really circumvents the Citadel Treatise on AI development, Creation and Implementation. Ends with the program complete, about to be installed.
Chapter 17 - Irina
Digitally, Irina is born on exactly the half-year anniversary of Shepard's death. Details the 'Project Derevko', both the station and Irina herself in her current form of being a Holoprojection from the Quantum Synaptic Processor 'bluebox'. Tali arrives and meets her, and the whole group begin watching Alex' DVD's in his house on Intai'sei.
Chapter 18 - Alias
In the short time since Irina was born a lot has happened, and Alex ever-prescient-like observation of Lazarus Cell has expanded to other Cerberus Cells. Only now, a situation is beginning, and Alex needs all the help he can get. It's time for him to take a new, temporary, identity. Jack Bristow is in the House.
Chapter 19 - Fusion
While Alex is on his mission, Tali oversees the creation of Irina's new body...
Chapter 20 - N3
Alex arrives at the new training facility on Arcturus, and begins the process to formalise his new status under the Alliance' MVC.
Chapter 21 - Resurrecting A Machine
Tali has returned to the Flotilla, but in her wake, Alex is left with new intelligence about the Lazarus Cell. Feeling up to a heist, 'Jack Bristow' and 'Laura Bristow' make way to the Minuteman Station.
Chapter 22 - A Twist in Fate
Returning from the heist, Alex and Irina find that there's a problem: A man from Alex' past is there, waiting for them, and he's not friendly.
Chapter 23 - Ascension
Alex is shocked when Tali sends him a message about Kahlee Sanders. Whatever the timeline should have been on that, it's different here, and only just beginning.
Chapter 24 - Jormangund
He'd always wondered how a company he'd bought stock in was able to manufacture the best Armour in the galaxy, armour that was ridiculously strong. But then, he'd not realised, until now, that they had a connection to the Collectors.
Chapter 25 - Hazard Operations
Before, they'd never gone against anyone wearing armour from Jormangund, but now they are, and they're realising just how bad it might be to go against the Collectors, given the connection.
Chapter 26 - Marina
Alex arrives back from some N4 training program, to a surprise new member of the group. Enter, his Daughter, Marina.
Chapter 27 - Laying the Foundation
Now head of the company, formerly known as 'Jormangund', Alex begins making ties with many elite forces across the galaxy, and finds it rather funny just who are assigned to representing the Alliance...
Chapter 28 - N4
No longer are the certifications done in simulations. Now it's time for a live mission. Is it just luck, however, that he's to attack a Cerberus Cell responsible for altering Paul Grayson?
Chapter 29 - Waking From Death
2 years. That's how long she's been 'Mostly Dead'. Well, now she's being woken, and wakes into a warzone. She's in a Cerberus base, and Mech's are loose. Guess it's time to meet up with Jacob, huh?
Chapter 30 - Station Lazarus
He lost contact with the Cerberus base, and Alex believes he knows why, and so he and Marina, on her first mission, head to the station to investigate. Is he just in time to be reunited with Shepard, though?