In this sequel, another spacecraft crashes on the planet ruled by apes, carrying astronaut Brent who searches for Taylor and discovers an underground city inhabited by mutated humans with psychic powers. Beneath the Planet of the Apes was a success at the box office but met with mixed reviews from critics. It was followed by Escape from the Planet of the Apes.
Following the events of Planet of the Apes, time-displaced astronaut Taylor (Charlton Heston) and the mute Nova (Linda Harrison) are riding on horseback through the desert of the Forbidden Zone. Without warning, fire shoots up from the ground and deep chasms open. Confused by the strange phenomenon, Taylor investigates a cliff wall and disappears before Nova's eyes.
Elsewhere in the Forbidden Zone, a second spaceship has crash landed after being sent to search for Taylor and his crew. Like Taylor's ship, it has traveled into Earth's distant future. However, surviving astronaut Brent (James Franciscus) believes he has traveled to another planet, and forward in time to the year 3955. He encounters Nova and notices she is wearing Taylor's dog tags. Hoping Taylor is still alive, he rides with her to Ape City, where he is shocked to discover the simian civilization. He observes the gorilla General Ursus (James Gregory) leading a rally calling for the apes to conquer the Forbidden Zone and use it as a potential food source, against the objections of the orangutan Dr. Zaius (Maurice Evans). Brent is wounded by a gorilla soldier and taken by Nova to the home of the chimpanzees Cornelius (David Watson) and Zira (Kim Hunter), who treat his wound and tell him of their time with Taylor. The humans hide when Dr. Zaius arrives and announces that he will accompany Ursus on the invasion of the Forbidden Zone.
Attempting to flee the city, Brent and Nova are captured by gorillas. Ursus orders they be used for target practice, but Zira helps them escape. They hide in a cave which Brent soon discovers is the ruins of the Queensboro Plaza station of the New York City Subway, making him realize that he has traveled through time to Earth's post-apocalyptic future. After following a humming sound deeper into the underground tunnels, Brent begins to hear voices telling him to kill Nova. Entering the remains of St. Patrick's Cathedral, he finds a population of telepathic humans who worship an ancient nuclear bomb.
Brent and Nova are captured and telepathically interrogated, and Brent reveals the apes are marching on the Forbidden Zone. The telepaths attempt to repel the apes by projecting illusions of fire and other horrors, as they had done to Taylor and Nova. Dr. Zaius sees through the illusions, however, and leads the ape army to the ruined city. With the apes closing in, the telepaths plan to detonate their "Divine Bomb" as a last resort. They hold a religious ceremony, at the height of which they remove their masks to reveal that they are in fact still-intelligent humans who are descended from survivors of the nuclear wars. The nuclear fallout has mutated them by removing layers of their skin, but greatly increased their psychic abilities.
Brent is separated from Nova and taken to a cell, where he finds Taylor. The mutant Ongaro (Don Pedro Colley) uses his telepathic powers to force Brent and Taylor to fight each other to the death. Nova escapes her guard and runs to the cell, screaming her first word: "Taylor!" This breaks Ongaro's concentration, freeing Brent and Taylor from his control. They then overpower and kill him. Brent describes the bomb the mutants worship and Taylor recognizes it as a "doomsday bomb", capable of destroying the planet, marked with the Greek letters Alpha and Omega on its casing.
The apes invade the subterranean city, making their way to the cathedral. One of the apes manages to kill Nova before being killed by Taylor and Brent. They are confronted by Méndez (Paul Richards), who raises the bomb into activation position before being gunned down. Brent and Taylor attempt to stop Ursus from accidentally setting off the weapon, but Taylor is shot. Brent manages to kill Ursus before being shot dead by the gorillas. The mortally wounded Taylor pleads with Dr. Zaius for help, but Zaius refuses, saying that man is only capable of destruction. In his last moment Taylor brings his hand down on the activation switch, triggering the bomb. The scene whites out and voiceover narration states: "In one of the countless billions of galaxies in the universe lies a medium-sized star, and one of its satellites, a green and insignificant planet, is now dead".
Soon after Planet of the Apes became a hit, a sequel started being considered by 20th Century Fox. Screenwriter Rod Serling was consulted, but his ideas did not interest the studio. Then the producers turned to the author of the original novel, Pierre Boulle, who wrote a draft for a sequel called Planet of the Men, where protagonist George Taylor would lead an uprising of the enslaved men to take back control from the apes as the gorilla general Ursus wants to fight humans. Boulle's script was rejected as it was felt that it lacked the "visual shock and the surprise" of the original. Associate producer Mort Abrahams then wrote story elements, and British writer Paul Dehn was hired to develop them into a script, tentatively called Planet of the Apes Revisited. Dehn implemented his trauma of the 1945 atomic bombings and the fear of nuclear warfare on the story. One of the elements thought up by Abrahams and Dehn was a half-human, half-ape child, but despite even going through make-up tests this was dropped due to the implication of bestiality. According to screenwriter Dehn the idea for Beneath came about from the end of the first movie which suggested that New York City was buried underground.
Although Charlton Heston showed little interest in reprising his role as Taylor, studio head Richard Zanuck thought the actor was essential to the sequel. After some disagreement with the actor's agents, Heston agreed to briefly appear with the provision that Taylor be killed and that Heston's pay go to charity. The writers decided to have Taylor disappear at the story's start and only return by the film's ending, and have a new protagonist for the major part of the story. James Franciscus accepted the role of Brent as a break from his usual TV fare.
Director Franklin J. Schaffner was invited to return to the series, but declined due to a commitment to Patton. Television and film director Ted Post was approached, and while objecting to the script for "not making a point at all", the producers asked what he did not like. Post then wrote a letter saying that "the loss of a planet is the loss of all hope". Post tried to get the other writer of the original, Michael Wilson, but a budget cut prevented him from doing so. Post and Franciscus - who wanted to help clarify the actions of and give depth to the character of Brent - spent a week rewriting the script, leading to over fifty pages of notes suggesting story ideas to fix some of the narrative problems in Paul Dehn's script.
Roddy McDowall could not return for his role in this sequel, because he was in Scotland directing Tam Lin. Actor David Watson portrayed Cornelius in this film with McDowall only appearing briefly in clips from the first film used during Beneath's pre-title sequence. Along with the animated series Return to the Planet of the Apes, this film is one of only two 1970s Planet of the Apes productions in which McDowall does not appear. Orson Welles was offered the role of General Ursus, but he turned it down objecting against spending all his screentime in a mask and make-up. The part ultimately went to James Gregory.
Before Zanuck was fired as studio president during production, he suggested that Post add an element suggested by Heston, the Alpha Omega doomsday bomb, to end the series. However, before the film's release, the producers were considering ideas for another sequel.
Production began in February 1969. The sequel, now titled Beneath the Planet of the Apes, had its budget reduced from $5 million to $2.5 million because Fox had suffered recently from several underperforming big-budget films, like Star!, Hello, Dolly! and Tora! Tora! Tora!. Nonetheless, the studio expected the film to return Fox to profitability.
Heston's parts were filmed in just eight days. The sets of the mutants' council chamber and the temple of the bomb were redresses of the Grand Central – 42nd Street station and hotel lobby sets from the film Hello, Dolly!
The original Apes composer, Jerry Goldsmith, was invited to write the score for the sequel, but Schaffner was using Goldsmith for Patton. Leonard Rosenman was hired to compose the score. Rosenman tried to blend Goldsmith's distinctive score with his own style, showcased in productions such as Fantastic Voyage. An official soundtrack LP was issued on the Amos Records label soon after the film's debut in 1970. For the LP, Rosenman was asked to rearrange his score for a smaller orchestra, adding contemporary elements such as electric guitar and rock percussion. These re-recorded pieces were interspersed with dialogue taken from the film. The soundtrack featured some of the leading Los Angeles studio musicians of the time, including bassist Carol Kaye and Moog pioneer Paul Beaver.
The novelization of the film by Michael Avallone retained the original scripted ending. Brent does not kill General Ursus. Taylor confronts him and Dr. Zaius. As Taylor tries to reason with Zaius, Zaius condemns him and Ursus repeatedly shoots Taylor with his pistol; Brent's rifle empties and the gorillas kill him. Ursus is horrified, telling Zaius that he has emptied the pistol into Taylor; he should be dead, but he still lives. Knowing he is dying, Taylor (after Zaius refuses to help him) decides to stop the violence by detonating the bomb. This he does, destroying the Earth itself.
Gold Key Comics produced an adaptation of Beneath the Planet of the Apes in 1970. This was the first comics publication in the Planet of the Apes franchise. Later, Marvel Comics published a different version in two series (b/w magazine 1974-77, color comic book 1975-76). Malibu Comics reprinted the Marvel adaptations when they had the license in the early 1990s.
Beneath the Planet of the Apes grossed $18,999,718 (approximately US $118M in 2016)  at the box office. The film holds a 41% "Rotten" rating at the film review aggregator website Rotten Tomatoes, based on 22 reviews. The film has a 6.1 (out of 10) rating from visitors to its IMDb page.