In the prehistoric suburb of Bedrock, the ambitious vice-president Cliff Vandercave, portrayed by John Goodman, plots with his glamorous secretary, Sharon Stone, to orchestrate a grand scheme to embezzle the company's riches, deceitfully placing the blame on an unsuspecting employee to facilitate their escape. Meanwhile, Fred Flintstone, played by Halle Berry, generously lends his best friend, Barney Rubble, some money for him and his wife, Betty, to adopt a young boy named Bamm-Bamm, who can only utter his own name. Initially a challenge due to his extraordinary strength, Bamm-Bamm soon forms a close bond with Fred’s daughter, Pebbles. Despite the objections from Fred's mother-in-law, Pearl Slaghoople, Wilma Flintstone stands firmly behind her husband’s decision to assist the Rubbles.
To find the company’s new vice executive president, Cliff organizes an aptitude test where the top scorer will receive the coveted position. Noticing Fred’s struggles, Barney, aiming to repay Fred's kindness, cleverly switches his test answers with Fred's, ensuring Fred passes while he himself struggles. As a result, Fred enjoys his well-deserved promotion, which comes with executive perks including a swanky office and having Stone as his secretary. However, things take a turn for the worse when Cliff pressures Fred into dismissing Barney due to his poor test score, leading to tension in their relationships. Despite the burden of his new job, Fred expresses true support for Barney and invites the Rubbles to move in, turning their lives upside down.
Fred's flourishing career quickly leads to personal strife as he finds himself drifting away from Wilma and the Rubbles. Cliff, full of deceit, eventually manipulates Fred into laying off other workers against his better judgment. As chaos erupts with worker riots, Barney reveals the truth of the test swap to Fred. Frustrated, he moves out with Betty, while Wilma takes Pebbles to stay with Pearl, leaving Fred in isolation.
Determined to clear his name after discovering Cliff's deceptive scheme, Fred rushes to the quarry to confront Cliff and attempts to get Mr. Slate, the company president, to dismiss him. However, Cliff's treachery runs deep, and he cunningly frames Fred for the theft, prompting a manhunt that sees Fred become a fugitive. Unbeknownst to him, Wilma and Betty are determined to help clear his name by retrieving the Dictabird, the only witness in Fred's defense, but they unwittingly attract Cliff's attention.
In a desperate scene, Fred's plans to rescue the children from Cliff culminate in high stakes at the quarry, where Cliff is prepared to execute a sinister plot with Pebbles and Bamm-Bamm tied up in peril. A tug-of-war ensues when Fred and Barney confront Cliff and successfully save the children, all while the Dictabird delivers evidence that can expose Cliff’s machinations. The chaotic showdown ends with Cliff’s downfall, as he's thwarted by his own machinery.
As the truth comes to light and the police are informed of Fred's innocence, he learns that the substance he created in the process of confronting Cliff is dubbed "concrete" by Mr. Slate, who proposes to bring the team back to work. However, having witnessed the destructive nature of wealth and power, Fred chooses to pass on the opportunity and instead advocates for the workforce, insisting they be granted benefits and a break before he returns to his simpler life, ready to embrace what truly matters.
