The first story is a Sheppard whump, ok all of them are, but this one is set before Common Ground, and yes it features Kolya. Sheppard and his team are ambushed off world by Kolya and a group of Genii, I believe Ronan is injured, like in the leg, but everyone makes it back to Atlantis except for Sheppard who is shot before he can make it to the gate. Kolya doesn't have him long as the team basically regroups and comes right back, they immediately redial back to the planet so that Kolya can't escape with Sheppard. I know it's not a long story but it was a really good one.
The next story has a very sadistic ancient who is conducting experiments and Sheppard's team gets caught in it. I remember they were fighting a bunch of soldiers, and then there was a flash of light, which is the ancient who seems to feed off the energy of those fighting. Almost like the Ori. Only the energy he takes happens to be Sheppard's life. It also knocks everyone out, when they come to the soldiers they had been fighting have vanished and Sheppard is basically dead. Teyla and Ronan work to resuscitate him while Rodney goes for the Jumper. I know they end being taken by the ancient who wants to feed off them, but makes them believe he didn't mean to kill John, and that they can help bring him back by sacrificing parts of themselves. Like Rodney gives up his intellect, I think Ronan his memories, I don't remember what he tries to take from Teyla. Through out this Sheppard is there but not physically, I think he's talking to another ancient trying to convince them to stop the bad ancient. Does this ring any bells?
And the last story is basically a Sheppard centric one, he's separated from his team on planet that only allows people with special papers to go through the gate. He is injured and taken in by an old woman who I think is named Maj, I remember she has some weird dragon like lizards as pets. There is also some weird wraith experiment that was left on the planet that produced a crazy animalistic wraith like creature that is going around killing people in the village that Maj lives in. It's a rather long story but I've tried different searches and can't find it.
Any ideas would be greatly appreciated!!