I had been thinking about a story where the player's crew will visit Vagra II and butt heads with the character Armus from the TNG episode "Skin of Evil." It might be very difficult to recreate Armus in the Foundry, but we'll see.
I was also thinking about a return of the Organians. I know they showed up in Enterprise...I'll just try not to think about that too much. They might not even show up, but it would be interesting to have a story back on the planet of Organia. Searching Organian ruins and looking for them. The title would be called something like "In Search of Mercy."
However, I was really thinking about putting together a six part story arc where a group of Starfleet captains, led by a couple Vulcans and Andorians rebel against the Federation. The leader of the group, a Vulcan Admiral, finds it illogical, after years of relative peace, the Federation is at war with the Klingons. And also fighting battles against the Romulans, Cardassians (or as my girlfriend calls them, the Kardashians...), Borg, Undine, Breen, Devidians, Terran Federation, and more to come. His goal isn't really just to create another enemy for the federation, but to overthrow the Federation council, and bring his logic to the Alpha quadrant. The way STO has shaped up, we haven't really seen a lot of turmoil within the Federation. It would also be a fun way to show off the new Vulcan and Andorian ships that'll be rolling out soon.
I have a klingon Boff on the FED side. His back story is that he was engineered in a lab and developed to infiltrate the empire and attack it from within. Sort of like a supersoldier. I want to explore his origin story somehow. That is my one of a thousand ideas
Okay today a new story arc epiphany hit me but since it is rough in mind i figured why not share the seed here.
Concept- a New "cult" emerges across the Alpha and beta quadrant- a cult that worship the Borg and see them as "deities" who are messengers from the divine seeking to bring every being together as one. The series of missions has Starfleet intelligence (not section 31, but actual intel,like difference between CIA and homeland security etc,though section 31 is more a unofficial MIA group but you get the analogy).send the players undercover to infiltrate the cult and try to locate its leader. The cult is being seen as a terrorist threat because whenever the group speaks out on some random Fed or Kdf world, it is followed by a trans warp cooridor opening at that location and a Borg raid assimilating the gathering "except" the cult members. This makes Starfleet believe the cult is working and cooordinating with cooperation from the Borg.
But as people will find common to my missions, there is always a twist....
Note- this series will attempt to justify and explain "why" the Borg collective even "has" a queen. (something thats been debated ever since First contact, i will not "define" the reason but "attempt " to offer a plausible explanation that is a belief system).