In 1988, Twentieth Century Fox executive Craig Baumgarten, impressed with Adam Rifkin's Never on Tuesday, brought Rifkin in to the studio to pitch ideas for films. Being a fan of the original Planet of the Apes, Fox commissioned Rifkin to write a sequel... "but not a sequel to the fifth film - an alternate sequel to the first film." The concept was that "the ape empire had reached its Roman era. A descendant of Charlton Heston's character would eventually lead a human slave revolt against the oppressive Roman-esque apes. A real sword-and-sandal spectacular, monkey style. 'Gladiator' did the same movie without the ape costumes. Having independent film experience, I promised I could write and direct a huge-looking film for a reasonable price and budget, like 'Aliens'." By September 1988 it was reported that Planet of the Apes: The Final Battle would be filmed the following year, with a Rifkin written and directed story "centering on the child of Cornelius' son and Taylor's daughter--the characters originally played by Roddy McDowall and Charlton Heston". The project was put on fast track and the vastly experienced Rick Baker was hired to design the prosthetic makeup, with Danny Elfman composing a film score. Tom Cruise and Charlie Sheen were considered for the lead role. Days before the film was to commence pre-production however, new studio executives arrived at Fox, which led to creative differences between Rifkin and the studio. Rifkin was asked to rewrite his Return to the Planet of the Apes script through various drafts. The first revision was dated 21 December 1988, "written by Adam Rifkin from a story by Cassian Elwes and Adam Rifkin." The film project was also referred to as 'Return to the Planet of the Apes: World At War'.
As a female narrator begins to tell her tale, the action opens in a desert, where a lone rider appears over the crest of a sand dune. He is General Izan, at the head of an army of gorillas, met on the sandy wastes by an opposing chimpanzee army. A bitter battle ensues before the narrative moves forward. In ‘Ape Square’ - the central plaza of Ape City - the ape civil war is about to be brought to an end. Decorated with medals, Minister Elizar Tafara is the overall gorilla leader, while the eye patch-wearing Secretary Nebb Gurio represents the chimps. Three orangutan judges - the eldest of the ape population and the last of their species - preside over the ceremony. Their leader, Dr. Zantheus, proclaims a great day for Apekind as peace has been restored. Just as the treaty is signed however, the symbolic handshake is ripped apart as General Izan's renegade gorillas open fire. They kill Tafara and Zantheus, and many other leaders. Gurio is injured and barely escapes.
The resumed war rages on in the desert. In Ape Square, chained and mute humans clean up the debris under the supervision of the gorillas, who control the city. Occasionally, the motorized military vehicles, which they have managed to restore, roll past. In Izan's military command headquarters, Cornelius bursts in, followed by two gorilla privates. He introduces himself as the head of the ‘Simiantarian Peace Organisation’, but Izan remembers him as the chimp "laughed out of his psychology and archeology positions for his absurd theories on anthropoid history". Cornelius pleads for peace, as he maintains the humans destroyed themselves in the same way many centuries earlier. As he is dragged out of Izan’s office by the privates, he offers to bring proof of the human civilisation. Amused, Izan gives his consent.
Shortly afterwards, Cornelius and his young son Pax travel into the Forbidden Zone. After a long search, avoiding the battlefields, they find no evidence. As Cornelius prepares to abandon his quest, the two are abducted by humans, who drag them into a system of underground tunnels leading to subterranean New York. There Cornelius is reunited with an old friend - Taylor, with his young son Duke ("named after John Wayne"), and Duke's friend Ariel. Duke’s mother has died (as, apparently, has Pax’s). To the amazement of Cornelius, both the human kids can speak. Taylor explains that he has spent his time in the Forbidden Zone teaching humans to speak, to read, to think. Cornelius witnesses a human called George teaching a class of humans. Taylor has written down what he remembers of human history, and tells Cornelius "I really miss movies... my favorite was 'Ben Hur'". He is reluctant to give Cornelius the proof he requires, as he has created a new human civilization free from the apes' domination and doesn’t want to endanger it.
Some time later, In the General Assembly Room of the ‘League of Anthropoid Nations’, Gurio and his chimpanzees face Izan and his gorillas in a heated exchange, supervised by the two surviving orangutan judges. Unexpectedly, Cornelius and Pax enter, carrying one of Taylor's hand-written history books. Izan, tiring of Cornelius, threatens to kill him, but the assembly falls into silence as Taylor himself enters and speaks. He reasons with them that they should learn a lesson from man’s stupidity. Suddenly, Izan stands and shoots Gurio dead, and any other chimps who openly defy him. His gorillas seize Taylor and Cornelius as Izan seizes Pax, swearing to raise him as his own son and heir, and to make this chimp child as mighty as a gorilla. Izan declares gorilla victory in the civil war, and his first act as self-appointed ‘Supreme Ruler of the Empire of the Apes’ is to order Taylor's execution. Cornelius - tasked by Taylor with raising his orphaned son - is exiled to the Forbidden Zone. His return will cause Pax's execution. As the years pass via a montage, we see Cornelius raise Duke. He reads Taylor's history books to Duke and Ariel, and other human kids - Dara, Charlie, Albert & Jonas - stories about the sinking of the 'Titanic', etc. An occasionally obstinate Duke practices shooting his father’s guns, to the anger of Cornelius. George the teacher devises an irrigation scheme to water the community’s crops. Dara and Charlie mature and become a couple, while Duke and Ariel resist their attraction to each other. After twenty years pass, the narrator of the movie is revealed to be Ariel.
Naturally for a society led by an archeologist, there is a strong focus on exploring the artifacts of the underground city. On one such dig, the tribe breaks through a wall and uncover a buried but almost untouched city street. One of the magazines in a kiosk has a picture of Taylor entering his craft, with the headline "Bon Voyage Taylor". Thus prompted, Duke demands that Cornelius tell him the truth about the ‘accident’ that caused his father's death. Duke becomes enraged upon learning the truth, accusing Cornelius of protecting his fellow-apes, but he is calmed by Ariel. He begins to dream about his father and about revenge.
In the renamed 'Izan Square' a massive military parade, reminiscent of those in Red Square millennia before, passes before Izan and his cold, ruthless and cunning adopted son Pax. While the entire population of the city is obliged to attend the rally, three chimps from the 'Simiantarian Liberation Movement' - Wynora, Liam and Orpheus - clobber a gorilla guard and free a group of caged human slaves. Taking them through the city's sewer system, they release them into the desert. The three chimps then rejoin their co-conspirators Miles, Wingding and Professor - an old colleague of Cornelius, and co-founder of this group that began as Cornelius’ Peace Organization - in their secret underground hideout. Later, a queue of gorilla, chimp and human prisoners are led to Izan Square's gallows for the daily spectacle of a public execution. Just as the city life follows a Roman model, Izan's court is an example of medieval debauchery. A 'fool' entertains his master, the gorilla lackeys humour Izan, while his son Pax accompanies a 'gorilla of the evening' to his opulent bedroom and drunkenly hints that things may be 'different' when he is in charge.
In the Forbidden Zone, Duke has disappeared. Ariel says she will go to the Ape City to find him, with or without help. Reluctantly, Cornelius agrees to go with her, fully aware of what the consequences could be. In a gladiatorial arena in the city, apes pay their hard-earned 'moques' to watch the bloodthirsty combat between three humans and a giant mutant gorilla named 'The Machine', who pulverises the humans into a bloody pulp. At the fight's conclusion, a shot rings out and hits Izan's shoulder. Duke fired from his hiding place atop one of the countless statues of Izan, but has failed to kill his target. Ape guards race to capture him, and after a long chase he is captured. Izan and Pax interrogate him and plan his public execution for the following day. That night, Pax visits Duke in his cell to question him further about what he knows of Pax’s real father. Later that night, the SLM free Duke and, after another prolonged chase, take him to their secret hideout. Seeking news about Cornelius, Professor decides he will go with Duke back to the Forbidden Zone. The next morning, gorilla guards somehow locate the secret hideout and take Duke and Wynora to the arena to face The Machine. They use their wits to evade him, eventually jumping into the crowd and making their way to the top tier in yet another chase. They escape by jumping to a flagpole and sliding down. The Machine, ordered by Izan, follows suit but his size causes the flagpole to snap and he plummets to the ground. In the Square outside the arena, Duke and Wynora find themselves faced with Ariel, Cornelius, and an army of humans on horseback. They try to make their escape but are quickly surrounded by apes.
Izan confronts Cornelius, taunting him and Duke, but then all the other humans present begin to speak and shout, confounding the ape population. Furious, Izan points his pistol at Pax, reminding Cornelius of his vow. Cornelius pleads to die in place of Pax, and Izan agrees, but orders Pax to kill his own father. Pax aims, but having been treated so callously by Izan, he cannot bring himself to fire. As Izan points his own pistol at Cornelius, Pax instead aims at Izan. Izan stops in disbelief, but before either can shoot, The Machine rears back to life and lurches towards them. As The Machine strangles the life from the old General as revenge for his years of brutality, Izan fires repeatedly into the giant's chest. Izan's neck snaps. Satisfied, The Machine slumps forward, dead. After a long pause, Pax declares himself new ruler, but decrees an era of peace and harmony for all apes and humans, with Cornelius at his side. He asks the help of Wynora, who has shown her bravery and wisdom. Everyone in the city rejoices at the end of the tyranny, while Duke and Ariel sit at the Statue of Liberty at dusk, and as Ariel's narration ends they ponder the future of the Planet of the Apes.
The screenplay shares some ideas with another proposed sequel to the first movie - Pierre Boulle's Planet of the Men. As in that treatment (which Rifkin almost certainly would not have seen), the potential of the first movie's ending is explored to it's logical conclusion - that a resurgent human population would eventually reassert itself and face down ape control. The manner in which this is undertaken is somewhat different however. While Boulle underlined his theme of the human race being essentially beyond redemption and incapable of restraint, Rifkin showed them to be far more virtuous, if still occasionally flawed. Rifkin also emphasised the brutality and ignorance of the gorillas, compared to the compassion and intellectual nature of (some of) the chimpanzees, sharpening the contrast between the ape species. The orangutans are completely written out of existence shortly into the film for some reason, while neither Zira nor Nova are mentioned at all (except for the aside that Duke's unnamed mother is dead). The use of titles such as 'Simiantarian Peace Organisation', 'Simiantarian Liberation Movement' and 'League of Anthropoid Nations' owe far more to twentieth-century culture than they do to any alien society, though it's worth remembering that the sequel that was made - Beneath the Planet of the Apes - was directly influenced by the then-current anti-war protests and student movements, the ape civilisations' origins having already been revealed to be a mimicry of humanity. The death of Taylor early on and the placement of Cornelius as perhaps the central heroic character is an unexpected direction, and while the plot twist of having both Duke and Pax raised and moulded by fathers-who-aren't-their-fathers is a clever device, the extent of Izan's malign influence on Pax isn't explored to any great extent, perhaps because of the sudden redemption necessary at the script's ending. The story is based around action and adventure, with plenty of dramatic chases and fight scenes, and the happy ending, unusual for an Apes film, seems to leave little room for any sequel, though Rifkin's treatment itself was largely self-contained with only a few direct links to it's predecessor. As with other Apes script treatments however, the urge to reference the famous imagery proved hard to resist, with Taylor mentioning his love of the movie Ben Hur (starring Charlton Heston), and the movie ending once again in the shadow of the Statue of Liberty. In addition, Cornelius tells the human children the story of the 'Titanic', the story with which almost-Apes producer James Cameron would coincidentally later strike box-office gold.
The project was ultimately abandoned by the production team at Fox. It is understood that John Landis offered to rescue the project by serving as executive producer, but was firmly turned down by Fox's Joe Roth. "I can't accurately describe in words the utter euphoria I felt knowing that I, Adam Rifkin, was going to be resurrecting the 'Planet of the Apes'. It all seemed too good to be true. I soon found out it was."