Orion was a code name for a CIA-sanctioned group for illegal operations.
It was created by the CIA so they could accomplish off-the-books operations; unlike SEAL's militia, Orion specialized with illegal and unsanctioned operations and missions that were too grisly to go through legitimate channels, such as assassinations and regime change, among others.
Douglas Winter found out about this illegal NSA program. Orion was shut down by Deputy Director of the CIA, Tom Carter, in order to erase any trace of it and its previous operations.
It is implied that Carter sent an attack to Orion's squad that killed everyone in Afghanistan, except for Jane.