«Across the Universe» by George Zebrowski,Pamela Sargent

The Hawking left Earth during the 21st Century on a one-way mission to colonize a distant world. Due to the relativistic effects of pre-warp travel, it's crew has aged only thirty years while two centuries have passed outside the ship. When the Starship Enterprise™ comes to the rescue of the malfunctioning Hawking, the colonists find themselves thrust into a universe and an era that has left them behind.
Captain Kirk intends to help the colonists adjust as best he can, but the task is not a simple one. The newcomers are survivors of a more violent, more paranoid time – and the have brought old suspicions, and an ancient weapon of mass destruction, into a world of unexpected challenges and dangers.