By 2018, the Ferrymen as we currently know it no longer exists. Here's how it all shook out:
In late 2011, with Pollepel Island the last Ferrymen bastion still standing, the Council voted for a large scale evacuation of its operatives and those under their care to Quebec. Someone within the organization (read: Griffin), disillusioned with the Council's leadership, tips the government off to the operation and General Heller sends 500 soldiers and 5 tanks to surround the island, preventing escape. A forcefield supplied by Malcolm protects the island until the 19th, when Griffin murders Malcolm and brings it down, allowing Heller's troops to storm the island.
The events of the Pollepel Siege finale will occur here. Since we haven't written it yet (next week!), I don't want to get into too much detail about how it pans out so there are still some surprises, but the majority of the people on the island escape. There are some notable casualties.
Thanks to the evacuation plan put in place by the Council and Special Activities, more than two hundred survivors successfully cross the border to Quebec. Some settle in Canada, while others are sent abroad where they are welcomed with open arms in France, Norway, and the U.K. where they are interviewed by the free press and the horrors of the Department of Evolved Affairs, the Institute, and the American military are fully brought to light. It is never disclosed who betrayed the organization to Heller.
2012 - 2014
During the civil war, the Special Activities division reunites to stage guerilla attacks on enemy forces. Because this was such a small contingency of the original Ferry, there are only a handful of Ferry operatives who participate in combat. Everyone else is either in hiding or has fled the country, much as it was when the organization was originally founded. After the war ends and Praegar becomes president, Praeger exonerates all surviving Ferrymen and offers state-sanctioned pardons in exchange for their testimony during the war tribunals. Some take small reparation payments of $25,000 to help resettle New York City inside the Safe Zone.
2014-2017
Former Ferry operatives who accept the deal come forward to testify during the war crime tribunals that target individuals who committed atrocities against the Evolved. Panels comprised of Ferrymen, well-meaning government officials, and affected citizens sentences dozens of people to death, including General Heller and James Muldoon (in spite of his actions assisting the Ferry in late 2011).
The majority of survivors are living relatively peaceful lives. It is estimated that the Ferry saved upwards of 15,000 individuals between 2007 and 2013. Those who are still mistrustful of the government have probably fallen in with Hana Gitelman's Wolfhound. Others may be working with Brian's new Lighthouse Initiative. Others still, who resettled int he Safe Zone, might be working as community leaders there. The faction, however, has not officially existed since the end of the civil war.
Members of the Ferry in 2018 are considered war heroes by many, even if the majority of their work occurred before 2012. Your character may have given interviews, or had books written about their stories. Once and awhile, a former Ferrymen turns up on the news having been murdered by anti-Evolved extremists. That sort of thing still happens with regular frequency despite SESA's best efforts.
Hit me up if you have any questions!