Okay, here's my plot for ME:A2 - The Kett Don't Strike Back
Major Arc: Starts as Kett mop up and consolidation of gains/building on investments. You do a couple missions to hold the alliances you've made together and to sit on the Roekaar. Maybe add the EOS independents or another newly discovered race (or faction of Milky way refugees) - or not. It is going too easy though. That is because instead of returning in force, the Kett have pulled back.
Arguing through the politics of just enjoying the victories pathfinder central, which has by now pieced together a pretty good idea of where Kett central is, wants to investigate. You've made progress on the scourge and remnant and are beginning to put together a plan to use them to defeat the Kett on their home turf but haven't quite figured out how to get those things there, or even what you're actually up against, or what the Kett are planning. Pathfinding team away.
Big trip works both ways.
You go to the Kett cluster and learn, through adventures against/with the Kett and their minions/servants (which are now also starting to run amok) that the Kett took what they learned from you about remnant home and put it to use. This drew the attention of the Jaardan and the "anti-Jaardan" which are proceeding to chew the Kett up and spit them out.
Your sibling has adventures dealing with what is now becoming a stream of refugees, some hostile, some just desperate, some Kett. Fit them in? Find room? Wipe them out? Try to add to alliances? Break them and form new ones? Coordinating your responses via SAM is the only way to make it work as a whole and your twin doesn't always agree - you have to kinda schizophrenically work it out with yourself.
Boss battle at the end is a fight against either just one of the Jaardan/anti-jaardan factions where you attempt to pick sides. This is complicated because you learn, through further remnant development and discovery, one of those groups is probably the benefactor and you're not sure which one.
Big hook at the end is it doesn't matter. You learn whichever one you backed is irrelevant, you just pruned a branch and made the tree angry. Others may think the wicked witch is dead.
Side plots/twists:
1) You find a remnant ship/station with Rachni or Yahg on it and evidence points as much to them originally being created by the Jaardan/anti-Jaardan and seeded like the Angara as to them being just copied for use... and the Angara are made to wonder again if they're constructs or a naturally evolving race that was copied from somewhere. Now you do too.
2) Do you continue to use remnant tech/scourge and, if so, how? It starts having ramifications and not all of them are positive anymore. You still don't fully understand why or how it works.
3) SAM is not your friend. Dad's fixation with your ma (and/or the introduction of the alien VI) put a twist in the logic like HAL. You have to deal with it and in the end either accept control, call it a quirk and repair it, or turn it off for good.
4) What is the plan to deal with the enemy? Do you:
- assemble a coalition?
-make a deal with the Kett?
-develop remnant/scourge assets?
-again cure the genophage and repeat the old deal with the Krogan?
-weaponize AI/VI as SAM hybrid?
What combination of those?
These decisions feel like they will carry over to the third installment for your options to deal with the bigger showdown. Biggest unanswered questions remain why you're here and what you should do about that.