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 New Earth Book 6: Challenger by Diane Carey
Far from the reaches of the Federation, the Starship Enterprise has been guiding the development of a once-obscure colony planet upon whose fate the future of the galaxy may now depend. The Enterprise has been the sole representative of the Federation, fighting a constant battle to protect the colonists from enemy aliens and standing alone against all those who have their own designs on the colony world.

Challenger

But all adventures come to an end. It is time for Captain Kirk and the Enterprise to turn over the guardianship of the colony to another ship and crew. The new ship arrives in the midst of a deadly attack on the colony–and is destroyed. With the Enterprise off fighting a new and powerful enemy that threatens the colony as well as its enemies, Commander Nick Keller, first officer and ranking survivor of the decimated crew, is marooned and at first alone–but he must find a way to complete his original mission and come to the aid of the Enterprise in what might be its most desperate hour.