Definitely McShep. Caldwell is actively trying to catch John and Rodney being inappropriate so that he can take John's place as military commander. When he finally gets enough proof he tries to blackmail Rodney even though he plans to get both out of Atlantis. Hermiod helps Rodney in getting back at Caldwell who refuses to give in so Rodney sneaks onto the Daedalus and poisons Caldwell. I just reread it a short time ago and now can't find it. Please help!
Found by danceswithgary. The Letter by Ellex
Found by danceswithgary. The Letter by Ellex