I did something similar to what Pericles did except I had the Kinshaya reappear in the neutral space shared between the Klingon Empire, the Romulan Empire and the First Federation.
It was for a Romulan Campaign and the crew had no idea what they were as their ship was crippled. They managed to escape the initial assault but along the way uncovered that the Klingons were apparently at war with this 'new' race.
Their actions in turn ended up causing massive friction between the Romulan and Klingon Empires which eventually led to a three-way border war and the end of what remained of the alliance between the two.
"It is our mission to push back the darkness from the light and expand the boundaries of knowledge and understanding. That doesn't mean exploring every pleasure planet between here and Andromeda XO."