For Greene's Star Trek: The Prospect Chronicles universe counterpart, see John Greene.

In the Pendragon universe, John Greene was the commanding officer of the USS Advantage.

By 2379, Greene had risen to the rank of Rear Admiral. In this same year, he, with former USS Prospect-A colleagues Anne Tedesco, Daniel Radke, Kari Eriksson and Hahn Jun-Seok, attended the new Deep Space 9's commissioning after Project Restoration. During this time, Radke convinced Greene to lead a task force to Myhr'an space to explore the possibility the Myhr'an could be under M'Tar influence. This command came in conjunction with Starfleet data supporting the possibility.

Starfleet only allowed Greene to take six starships in the fleet, so he reassigned Fack to accompany Noah Wrightson aboard the USS Cantabrian as Wrightson's experiences with the M'Tar were nil.

Upon discovering the Myhr'an were planning on destroying the Federation planet Rhaandaran, Greene ordered the fleet to intercept the Myhr'an. (Star Trek: Pendragon: Other Knights anthology: "Gravity")

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