«Double, Double» by Michael Jan Friedman

DOUBLE, DOUBLE
On a routine exploratory mission, the Starship U.S.S. Hood picks up a distress signal from a research expedition thought lost long ago – the expedition of Dr. Roger Korby, one of the centuries' greatest scientific minds. Korby himself is dead, it seems, but his colleagues have made a most incredible discover – a discovery they insist the Hood's captain see for himself. Reluctantly, the captain agrees to beam down…
Meanwhile, the crew of the U.S.S. Enterprise™ begins long-overdue shore leave on Tranquility Seven. James T. Kirk is looking forward to a few days of rest and relaxation….until what seems like a bizarre case of mistaken identity plunges Kirk into a whirlpool of mayhem and murder.
And puts an inhuman stranger with his memories and anilities in command of the Enterprise.