It's the series that started it all, lasting from 1999 to the summer of 2000, many epilogues of note are the Hero's Convention starring many of the top Megaman webmasters at the time (many you probably haven't heard of until now) and the crossover between the Sinister Six and the X-Force, the first time two teams crossed over into each other's series. It's also famous because it is the first series where a major character died.

Unless otherwise noted, these stories are written by Gary

Sinister Six: Issue 0-The Sinister Six Lost Episode (Very first Epilogue)
Sinister Six: Issue 1-The Sinister Six VS Super Chaos
Sinister Six: Issue 2-The Sinister Six Get Musical
Sinister Six: Issue 3- Mega Man Trivia
Sinister Six: Issue 4-The Mega Man Hero's Convention
Sinister Six: Issue 5- All I want for Christmas
Sinister Six: Issue 6-Yahoo Auctions Staring Gary! (Written by Tim)
Sinister Six: Issue 7-Sinister Six Cartoon Show!
Sinister Six: Issue 8-Tale Of Two Teams (Co-Writen by Ben) (4 Chapters, including Promo)
Sinister Six: Issue 9-Edward's Funeral!