Choice A: Starting from Calamity Trigger after the opening timeskip, where Ragna and Noel arrive in Kagutsuchi. Takamagahara does not exist, so deaths are permanent (unless revoked by science or magic) and choices are final.
Once you reach the Cauldron, be very careful what you do. From that point on, the stories of Continuum Shift and Chrono Phantasma follow.
Choice B: Time is distorted by the events following Chrono Phantasma and a majority of the characters are in the era of the Dark War- their memories are fragmented, but not to the point where they don´t remember anything, and their goal is to get back to their own time as soon as possible, while the remaining characters try their hardest to battle Terumi and his minions, who is preparing nothing short of the apocalypse- more specificly, ultimate despair for each and every person in the world.
Choice C: Terumi has taken over Hazama`s body at long last and has gone missing, in the meantime Saya`s activities are alarming- though public appearances, she´s steering the country into a civil war against Ragna and Sector Seven, to either secure their arsenal or force them to use it, creating the world of death she desired.
Meanwhile, the Murakumos thought dead are reviving one after another, a side effect of Amaterasu´s destruction, and those who are still under NOL control are given orders to stop the civil war through the use of violence. Top priority would be to find Saya and stop her, secondaryly, find Terumi and stop the Murakumos before they can slaughter the masses.
Choice D: Deadpool joins the character roster. Kokonoe then sets out to find a way to kill him, as she wanted to be playable instead. Meanwhile, all of the girls are being annoyed by the scarred merc with a mouth, and Ragna´s job is becoming significantly more difficult with the mercenary running around as a vigilante and gun for hire.
Choice E: Ponies
Choice F: The Reapers invade. Survive at all costs while trying to find a way to stop their relentless destruction.
Choice G: Lost town rebells. In their futile quest to return the sun to their world, they`ve decided to take it by force and oppose the NOL. As they multiply asexually, the NOL cannot erase them all, and the fact that Jubei and Ragna protects them makes it a significant danger.