Mr. Spinrad was paid about $5,000. Then, he told the CBS-owned Startrek.com, the producer Gene Coon “rewrote it into an unfunny comedy,” and at his insistence, the “Star Trek” executive producer and creator, Gene Roddenberry, killed the project.

Dorothy Fontana, a former “Star Trek” story editor, said, “I do remember both Genes saying, ‘It’s not working.’ ”

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Mr. Spinrad soon donated his sole copy of “He Walked Among Us” and other papers to California State University, Fullerton. With several other drafts of the script, it lay in the archives for decades. Sharon Perry, the university’s archivist and special collections librarian, said she had received only one inquiry about “He Walked Among Us” in her 27 years there.

But in October, at the annual New York City Collectible Paperback and Pulp Fiction Expo, a man seeking Mr. Spinrad’s autograph showed up with a copy of the script, which he said he found at another convention. A few months later Mr. Spinrad began selling the script on Amazon and Barnesandnoble.com, and the producers of “Star Trek New Voyages: Phase II” learned of it.

Based in Ticonderoga, N.Y., “Phase II” is one of numerous fan-generated “Star Trek” Internet series, this one named for “Star Trek Phase II,” Mr. Roddenberry’s failed 1977 attempt to revive his creation for television. This Web series is distinguished by its fidelity to the original’s sets, costumes, props, music and other elements, as well as appearances by some original cast members and new stories by writers like Ms. Fontana.

Over the years CBS gained the television, online and merchandising rights to “Star Trek.” But because the “Phase II” cast and crew make no money from their work, the network usually allows them to indulge their hobby.

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Around the time Mr. Spinrad offered “He Walked Among Us” online (confusingly he published an unrelated novel with the same title in 2010) he arranged with the “Phase II” senior executive producer, James Cawley, who also portrays Captain Kirk, to film it. The writer said he was “blown away” by the series and planned to direct the episode himself next fall.

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But this month, Mr. Cawley said, CBS asked him in an e-mail to cease and desist. CBS also contacted Mr. Spinrad, who withdrew “He Walked Among Us” from the Internet.

The network said it was now “considering opportunities to offer licensed copies of the work.”

“We fully appreciate and respect the passion and creativity of the ‘Star Trek’ fan and creative communities,” CBS said in a statement. “This is simply a case of protecting our copyrighted material and the situation has been amicably resolved.”

By all indications CBS is within its rights. In the entertainment industry the paid writer of a teleplay generally cedes the rights to the material, even if it remains unproduced.

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And Mr. Cawley said: “I’m not going to do anything that might be questionable. I have such a good relationship with CBS that I can call them anytime and ask, ‘Is this a problem?’ ”

Still, in interviews fans said they were dismayed that the network had scuttled a heartfelt homage to a beloved program.

“I can understand their legal rights,” said Erik Pless, a lawyer in Green Bay, Wis. “But it strikes me as heavy-handed. No one is profiting on this.”

Other fans pointed out that “Phase II” has already produced an unused script, by David Gerrold, the author of the humorous 1967 “Star Trek” episode “The Trouble With Tribbles.” In 1987 his “Blood and Fire” was shelved by “Star Trek: The Next Generation”; he reworked and directed it for “Phase II” in 2007 and never heard any objections.

“I don’t understand CBS’s thinking on this at all,” Mr. Gerrold said. “They didn’t care then. Why do they care now?”

Mr. Gerrold predicted a Trekkie backlash. “ ‘Star Trek’ fans,” he said, “are not a sleeping dragon that you want to poke.”