Benji, who I will shift into PC status, will find herself unable to let go of the fight after Pollepel Island. She will be deeply involved in the war efforts, abusing her ability to extract intelligence, coerce, and locate persons of interest through Inception-style dirty tactics, and isn't afraid of showing up in person either. By the time the war has finished, she won't be done with it, and continues to hunt down war criminals who escaped trial as well as targetting anti-Evo extremist groups, disseminating information to those who can neutralise them.
She is likely to be involved with Wolfhound, and some Bonnie and Clyde type murderous shenanigans with Calvin whether he is also involved or not. In her view, apology from the United States is insufficient, and her job in having come back from the future is not done, even seven years down the track.
Joseph is a WIP with regards to what happens to him in the immediate early days and war. Will contact his close relps and friendships and hash some stuff out. Possibly he will start off with the Lighthouse Initiative, once that's established.
By 2018, though, since reparations began, Joseph picked up qualifications to become a mental health counselor. He already had a masters under his belt from Jesus School back in the day, and along with government reparations, managed to attend some postgrad study to work with SLC-expressive youth. He is currently still practicing under supervision, but will be done in another year or so. He is still an avid Christian and most know of his history as a pastor, which earns some nicknames, but has stepped back from doing any evangelicising or church leading for now.
He is a council member of the Safe Zone Cooperative. His daughter, Hannah, is about eight years old, and lives with himself and Kaylee. His connections with action and adventure are almost entirely through Kaylee's activities, but has opened his door to any friend from before the wars, and is known to give visions to those who need them.
Gabriel vanished after the siege of Pollepel Island, using the cover of Sylar's apparent destruction to his benefit. To this day, it's unclear to some whether he was responsible for the second New York bombing or not, although those that knew of his clone problem can probably form correct conclusions. During the war, he probably continued to negotiate the line between hero and monster, becoming more and more abstracted from his more human side until he eventually couldn't take it anymore when nothing managed to kill him.
He is now living in a depression cabin in the mountains, trying to work out how to end his life. Party!
Logan will be living in the Safe Zone. He owns an antique shop. He launders money, and gambles, and is slinking into the developing criminal underground, being his favoured terrain. He leaves a porch light on for Hana, and sticks close with the Kozlows.
During the war, he was probably involved with fighting back, his ability having mutated ever since he lost it and regained it into a strange but very useful wide spread version ideal for more distanced combat as well as medical assistance. He was apprehended at some point, and testified in the war tribunals against Heller, and due to the fact he'd been slated for execution during the events of Eltingville, he came down on the right side of history, landing on his feet. Because of course.
Francois is a mystery, for now. But if Teo goes off on his own for any length of time, he will definitely sleep with someone.