Pre-production work started, with sets built, several television grade models (including the Enterprise herself and many of the pilot episode's models) made, deals made to bring back most of the original series cast, and several actors cast. It was planned to use the original series uniforms. Principal photography had not started, but test footage had been shot. Story writing had proceeded to thirteen scripts, enough for a half-season.
Work on the series came to an end when the proposed Paramount Television Service folded. However, following the success of the science fiction movies Star Wars Episode IV: A New Hope and Close Encounters of the Third Kind, the planned pilot episode entitled "In Thy Image was adapted into a theatrical production, Star Trek: The Motion Picture.
According to the series Bible, Xon was to be a full Vulcan, unlike Spock, and fresh out of the Academy at 22. Doctor McCoy was to have been protective about him. The character of Xon did not appear in The Motion Picture, although David Gautreaux had been cast in the role. When Leonard Nimoy finally agreed to reprise Spock, his Vulcan replacement as Science Officer became Commander Sonak, and appeared briefly in the film; after only a few lines of dialogue, he was killed in a transporter accident. This was to preserve Xon, and the actor who had so carefully developed him, for a possible future production. David Gautreaux made a cameo appearance in the movie as a human, Epsilon 9's Commander Branch.
The concept of the brilliant young Vulcan scientist, Xon, almost survived into a later movie. One premise developed as a possible sequel to the first movie included a male Vulcan called Doctor Savik. A variation of that name, Saavik, was later given to a female Vulcan when elements of several premises were combined for Star Trek II: The Wrath of Khan.
Ilia, a Deltan, is established as an empath. Both the Decker and Ilia characters appear in The Motion Picture, although neither of them survive it. The Motion Picture establishes that Decker and Ilia had a pre-existing relationship. Persis Khambatta was cast as Ilia for Phase II and was carried over onto the film. The TNG characters William T. Riker and Deanna Troi are derived from Decker and Ilia.
A number of screen-test shots of Persis Khambatta in Ilia makeup were taken, as well as footage of costume tests.
Several episodes of Star Trek: Phase II were scripted:
|"In Thy Image"||Alan Dean Foster||The two-hour pilot that eventually became Star Trek: The Motion Picture. Alan Dean Foster's story outline was based on a premise written by Gene Roddenberry for Genesis 2, named "Robot's Return". A huge starship crosses the universe looking for its creator on Earth.|
|"Tomorrow and the Stars"||Larry Alexander||During a Klingon attack, Kirk orders an emergency beamup and is transported to Pearl Harbor, Hawaii just before the Japanese attack on Pearl Harbor and falls in love with a woman living there. The plot is similar to that of the 1980 film The Final Countdown and of the Original Series episode "The City on the Edge of Forever" .|
|"Cassandra"||Theodore Sturgeon||The Enterprise mediates a dispute between two worlds over "The Monitor", while a clumsy ensign takes care of an infant alien who can foretell the future. Based on the story of Cassandra.|
|"The Child"||Jaron Summers and Jon Povill||A being of light impregnates Ilia to experience life as a Deltan. The Enterprise's hull begins to fail as they come across a strange nebula. The idea for this episode was later used as the basis for a Next Generation episode of the same name.|
|"Deadlock"||David Ambrose||While searching for a missing starship, the Enterprise is recalled to a Starbase to engage in a very strange war game.|
|"Kitumba"||John Meredyth Lucas||The Enterprise is sent to the Klingon homeworld to help Ksia, the underage Klingon leader, stop his regent from making war on the Federation. This would have been a two-part episode.|
|"Practice in Waking"||Richard Bach||The Enterprise comes across a sleeper ship where Decker, Scotty, and Sulu get trapped in a simulation of the 16th century witch burnings.|
|"The Savage Syndrome"||Margaret Armen and Alfred Harris||While investigating an ancient starship, the Enterprise is hit with a blinding light which brainwashes the crew, reverting them to savages. A similar situation was featured in episode 15 of Space: 1999 and in the Next Generation episode Genesis.|
|"Are Unheard Melodies Sweet?" or "Home"||Worley Thorne||While searching for a missing starship, the Enterprise comes across a world in need of men.|
|"Devil's Due"||William Douglas Lansford||The Enterprise has a first contact with the planet Neuterra just as a mythical creature, Komether, who was sold the planet in exchange for peace millennia earlier, appears. The idea for this episode was later used as the basis for a Next Generation episode of the same name.|
|"Lord Bobby's Obsession"||Shimon Wincelberg||The Enterprise comes across a derelict Klingon Cruiser with one life form aboard - one Lord Bobby from Earth's late 19th century.|
|"To Attain the All"||Norman Spinrad||The Enterprise gets caught in a solar system sized logic game where, if you win, you "attain the All," a huge repository of knowledge.|
|"The War to End All Wars"||Arthur Bernard Lewis||Derived from part of a discarded script treatment about warring androids on the planet Shadir ("A War to End Wars" by Richard Bach), the Enterprise rescues a female android, Yra, whose planet's successful philosophy of "peace through war" has been corrupted by a leader named Plateous III.|
Several writers, including Shimon Wincelberg, Norman Spinrad, Theodore Sturgeon, Margaret Armen, and John Meredyth Lucas had written Star Trek episodes before. Worley Thorne would get story credit on, and wrote the teleplay for, the first season TNG episode "Justice".
Additionally, as a tribute to this unrealized series, the fan series Star Trek: New Voyages changed its name to Star Trek: Phase II on February 16, 2008. The series will feature design changes from The Original Series to designs planned for Phase II, including a slightly refitted Enterprise and the introduction of Lieutenant Xon.