The story of ME1 for Duet Effect.
Duet Effect Plot points
Normandy: John CO, Kat XO (officially), Co-Commanding officers (reality).
Therum: John - Takes Kaidan and Wrex. Rescues Liara. Upon returning to ship, Kat has her put under guard until she is satisfied Liara is not a threat. John concurs with the statement. In a private discussion, Liara accesses John's memories of the Beacon, and uncovers hints about Project Janus (will discuss later).
Pinnacle Station: In the interim, the Normandy is resupplied at Pinnacle where John and Katelyn meet up with Roxanne Pierce. A fellow N7 who tied John for second place in their N7 graduate rankings and instructor for recruits at Pinnacle. Ahern challenges the three top N7s to his special simulation and we have more light shed on their past. John used to no-nonsense and without humour, while Kat used to be quiet and notoriously grim. They beat the simulation with flying colours and spend the rest of the night reminiscing and poking fun at their younger days.
Feros: Kat and John handle initial colony mission. Ashley and Garrus go with John across the highway, Kat stays behind to support colonists. They turn on her and tries to forcibly enthral her to the Thorian. She uses her biotics and barely makes it back to the Normandy. John finishes off the Thorian and Katelyn is in quarantine for a week.
Interim: Liara having now linked with John again, gets the second round of information and even more glimpses of Project Janus. She asks him about it privately, John threatens to kill her if she mentions it again.
Noveria: Kat and John tag along for this one. Liara is the third. Benezia is killed and John opts to kill the Rachni Queen. Kat opts to kill it too, but backs out at the last possible second, justifying that she'd hunt the Queen down herself if it caused any more trouble.
Result: A massive falling out between Kat and John professionally. John calls her out for making stupid decisions against his orders and Kat defends her decision.
Spinning wheels: With no more leads to go on, Normandy is adrift and neither Shepard is willing to spend two minutes in the room with the other. Then Bring Down The Sky happens. Kat and John opt to do this mission, Garrus acting as their third. They save the colony over arresting Balak and after the mission, John compares Kat's decision to join them to the Torfan offensive, Kat denies this. The discussion devolves into sibling banter and the two reconcile.
Virmire: Wrex is talked down from attacking John. Ashley is sent with Salarians, John and Kat take as much heat off them as possible. At the vital decision, the twins split up. Kat takes off to support Ashley and the Salarians, while John saves Kaidan. Using Saren's confrontation as distraction, Kat saves the Salarians and escorts them back.
When they escape, a Geth head-shots Katelyn. Her helmet absorbed most of the blow but she's critically wounded and her left eye, its socket are destroyed, her arm is also severed. Post briefing, John and Liara have a private discussion, where he apologises for his earlier behaviour but requests she forget about Project Janus.
Ilos: John hunts down Saren, but his feelings are no longer of duty but vengeance. Meeting with Vigil, John takes Garrus and Kaidan on the final mission. Saren is dared to out-will the Reapers and Anderson is put in the Council.
Post Ilos: Kat is revived after the battle, and spends 3 months in hospital+rehab. John is killed one month prior to her release. Kat does not attend the funeral.
(note - this WAS gonna be brought up in the Citadel DLC, not before) Project Janus: After his death, some disturbing things come to light about John Shepard - namely, before 2172, no such person existed. Project Janus - named after the two faced god - was a program designed to rehabilitate hardened criminals and convicts into soldiers of the Alliance. Part of it included going so far as memory wipes. John and Katelyn Shepard's real names are Mark and Jennifer Aldrin, notorious mass murdering siblings from the slums of Ottawa.
They were given the choice of execution or enlistment when they were caught, which lead to the 'creation/birth' of Kat and John Shepard.
That's the basic points of Duet Effect's first arc. Sadly, not working on it anymore.