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Book Three of the series: The Great Below.
Prior to Michael's escape from M8G-352 Dr. Gwen Reyes confesses to what really happened between Michael and her during his escape attempted which resulted in the death of Sergeant Andrew Cole. Bound by the consequences of her actions, Gwen throws herself into Michael's work at the request of Lieutenant Colonel John Sheppard in the hopes to make up for her one mistake. As the years painfully pass and possibly millions in the Pegasus Galaxy suffer under Michael's descent into possible madness and the all-consuming need for revenge, Gwen's love for him twists into hatred. During that time a growing friendship with John becomes one of her few comforts. Now with Atlantis returning from Earth and Michael long dead, John and Gwen struggle to move on but one more of Michael's labs has yet to be explored. (Warning: Character Deaths and Adult Themes)

Published: 04 Aug 2011 Updated: 26 Nov 2011
Story Notes:Spoilers for the following Episodes:

Season 2: Michael and Allies,
Season 3: No Man's Land and Misbegotten
Season 5: The Prodigal

I'm sure I missed a few but basically this story relates mostly to anything involving Michael.

1. Prologue: Beside You In Time by Cease_Sphire [ - ] (2017 words)
A few months after the incident on the planet: M8G-352 Gwen tries to move on but begins to have nightmares about Michael. Warning this chapter contains: Consensual Sexual Content and unrelated Non-Consensual Torture.
Published: 04 Aug 2011 Updated: 11 Jan 2012

2. Chapter 1: The day the world went away by Cease_Sphire [ - ] (2938 words)
Michael returns to Atlantis one last time seeking only revenge and Teyla's child.
Published: 05 Aug 2011 Updated: 11 Jan 2012

3. Chapter 2: And all that could have been by Cease_Sphire [ - ] (2703 words)
Michael remembers Gwen but its too late.
Spoilers to The Prodigal (season five) and Sanctuary (season 1) (Warning: Character Death)
Published: 05 Aug 2011 Updated: 01 Jun 2012

4. Chapter 3: The Persistence of Loss by Cease_Sphire [ - ] (3109 words)
Gwen needs to see his body and say goodbye.
(Warnings: Nothing really graphic but again she views his body.)
Published: 07 Aug 2011 Updated: 01 Jun 2012

5. Chapter 4: The world has closed her eyes by Cease_Sphire [ - ] (3606 words)
A little bit of shore leave changes everything.
Spoiler to Enemy at the Gate (series finale) (Warning: Adult sexual content)
Published: 05 Aug 2011 Updated: 11 Jan 2012

6. Chapter 5: The Way Out Is Through by Cease_Sphire [ - ] (4261 words)
The team and Gwen explore one of Michael's first lab's.
Published: 05 Aug 2011 Updated: 01 Jun 2012

7. Chapter 6: The Wretched by Cease_Sphire [ - ] (4123 words)
What is found in Michael's lab complicates everything.
Published: 26 Oct 2011 Updated: 11 Jan 2012