Star Trek: The Original Series/Behind the scenes/Pilots/First

In early October, the production team began preparations for filming "The Cage." Several changes were made to the crew: Roddenberry appointed Morris Chapnick, a colleague from The Lieutenant, as his assistant. Pato Guzman returned to Chile and was succeeded by Franz Bachelin. Matt Jefferies completed the designs for the Enterprise, along with various props and interiors. By , the sets were ready for construction on stages 14, 15, and 16 at Culver Studios. Roddenberry was dissatisfied with these stages due to their uneven floors and lack of soundproofing—a remnant of the silent film era. Ultimately, in , the remainder of the series was filmed on Paramount stages 9 and 10, which were in better condition.
Casting the characters posed no issue, except for the lead role of Captain Pike, initially called "Captain April" and later "Captain Winter," before settling on "Pike." Roddenberry persuaded Jeffrey Hunter to take on the role. Leonard Nimoy, known for his work with Roddenberry on The Lieutenant, was cast as Spock. Majel Barrett, another The Lieutenant alum, was chosen as the ship's first female officer, Number One. John Hoyt, a seasoned actor in science fiction and fantasy, was selected for the role of Doctor Phil Boyce. Peter Duryea and Laurel Goodwin were cast as José Tyler and Yeoman J.M. Colt, respectively. The extras represented a range of ethnic backgrounds, marking a significant step for integration in the 1960s television landscape, where segregation was still prevalent in the United States. 
For the pilot episode's production, Robert H. Justman was recruited as the assistant director, having recently worked on . Makeup artist Fred Phillips also joined, tasked initially with creating Spock's iconic ears. Byron Haskin, another alumnus, came on board as an associate producer. The first scenes of "The Cage" (temporarily known as "The Menagerie") commenced filming on . Although the schedule was set for eleven days, the shoot ran significantly over budget and time, extending to sixteen days with a total cost of US$164,248 plus additional expenses.
However, many visual effects remained to be completed. The eleven-foot filming model of the , designed by Matt Jefferies, was constructed by Richard Datin, Mel Keys, and Vern Sion at Volmer Jensen's . It was then delivered to the Howard Anderson Company on .
In , the final version of The Cage was delivered to NBC and screened in New York City. The NBC officials were impressed with the first pilot. Desilu's Herb Solow remarked that NBC was astonished by its realistic appearance, calling it "the most fantastic thing we've ever seen." The pilot was rejected because it was thought to appeal to only a niche audience, and NBC desired more action and adventure. Concerns were also raised about Spock's "satanic" appearance and the female first officer, Number One. Nevertheless, NBC believed that Star Trek had the potential for a television series, acknowledging their own mistake in selecting The Cage script from the three original pitches. Having invested US$630,000 in The Cage, the most expensive TV pilot of its time, they did not want the funds to go to waste. Consequently, NBC took the extraordinary step of commissioning a second pilot.