Covenant: Mulder & Scully have to come to term with some changes. Takes place before Leonard Betts.
Covenant II: Monsters: Sequel to "Covenant". While exploring all the levels of their 'new' partnership Scully takes on a case involving deaths strange enough no one can deny they are X-Files. Their only link, abused children. Their only lead. A child who can see Mulder. Not all Monsters live in closets.
Covenant III: Death and the Maiden: This is a bonus extra for those who can't get enough glowing blue Mulder, but it WAS NEVER COMPLETED. The extra 7,000 words are not included in the overall word count.
This is a classic fic by Rhondda, but I never knew it continued after the original story until it was mentioned recently on facebook. I then discovered a part 3, but sadly it was shelved so Rhondda could finish other ongoing stories and never picked back up. Consequently you won't find it online.
I'm pretty sure JJ (cover artist) is Julie Jekel, but I'm too tired to delve into confirming that right now.