Came back after a year...decided to work on my Fed toon...supposedly Federation content was more fleshed out than Klingon, and it certainly seemed that before I left, but. When I finished off my few DS9 sector missions, no new mission chains are popping up. Where does a mid level Fed captain get his quests at?
The problem is that when they introduced the episode replay feature they also opted to remove the "Patrol" missions. Now, the special patrols are still there but the mission givers do not tell you about them (no clue why). So one option is to wonder around a level appropriate zone and check each system to see if it has a patrol mission. Alternatively head to the nearest star cluster and do the exploration missions there.
The other option is to replay the story missions using episode replay.