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In the final scenes of TNG: "Transfigurations" (after meeting with Zalkonian ship), The Zalkonian Commander Sunad explains, that they have hunted down small ship, on which the alien ("John Doe") and three others escaped Zalkonian home planet, destroyed it and killed all abroad. The fact, that Enterprise crew has rescued John Doe was a real surprise to Sunad.

It doesn't make sense to me, what, in this situation, caused Zalkonian ship to return to the place, where they once destroyed refugees' ship? If they were so sure, that both ship and entire crew was eliminated, that shouldn't have any reasons to return. There's also no sign in the episode about anything, that would let them change their mind / become suspicious / detect the alien.

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The Zalkonians didn't return to the crash site, they were heading towards the Enterprise:

Sunad: I am Commander Sunad of Zalkon. You are trespassing into our space and you are holding a Zalkonian citizen.

Picard: I'm Captain Jean-Luc Picard of the United Federation of Planets. We do not intend transgression of-

Sunad: You will return him to us immediately.

Note that they only answered the hail after scanning the Enterprise; they probably didn't know any of their people were on the Enterprise until afterwards, and didn't know specifically who it was until after communication was established.

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