The Goonies, a group of friends living in the "Goon Docks" neighborhood of Astoria, Oregon, face foreclosure on their families' homes from the expanding Astoria Country Club. On one of their last days their morale sinks particularly low due to Mikey's older brother having failed his driver's license exam, thwarting their plans to "cruise the coast in style" during their "last Goonies weekend." While rummaging through the Walshs' attic, they find an old newspaper clipping, a Spanish map, and an artifact relating to a rumor of a lost but not forgotten pirate treasure somewhere in the area. Hearing the call of adventure, Mikey tries to persuade his friends to join him in search for the treasure hoarded by a pirate named One-Eyed Willie. Initially reluctant, the group eventually decides to evade the authority of Mikey's older brother, Brandon, and escape for one last "Goonie adventure".

They head down the coast and stumble upon a derelict seaside restaurant that seems to match coordinates set by the map and an old doubloon, unaware that the Fratellis, a family of fugitives, are using the restaurant as their hideout. After first encountering the family, the Goonies come back after the Fratellis have left and discover their criminal intents, and send Chunk, the group's clumsy, heavy-set dreamer and teller of tall tales, to get help. However, the Fratellis return before they can leave, forcing the Goonies to use a cavern underneath the restaurant to escape. The Fratellis capture Chunk and interrogate him, learning nothing until a pack of bats burst out of the cavern beneath the restaurant. Chunk is placed in the same room with the forsaken and deformed Fratelli brother, Sloth, while the rest of the Fratellis enter the cavern and follow the Goonies' trail.

As the Goonies traverse the cavern, Mikey discovers that it matches up with the map and convinces the rest of the group to continue to follow it to find the treasure. They overcome many deadly traps set by One-Eyed Willie, and eventually arrive at a large underground cavern and a lagoon where Willie's ship, the Inferno, lies waiting. While others begin to fill their pockets with the riches on the ship, Mikey finds Willie's skeleton, and reverently acknowledges him as the "first Goonie", leaving part of the treasure with him as tribute. However, as the Goonies exit the hold, they are caught by the Fratellis, who take their treasure and force the kids to walk the plank. The Goonies are saved by the timely arrival of Chunk and Sloth, now close friends, who help the rest of the group to shore. With the children no longer a threat, the Fratellis ransack the rest of the ship, including the share of the treasure Mikey left for Willie. This sets off a final booby trap, causing the cave to begin collapsing. The Goonies flee through a hole in the cave, finding themselves on a beach. Two passing policemen spot them and call in for help.

The Goonies are soon reunited with their parents while the Fratellis are arrested and Chunk offers to take Sloth into his home. As Mikey frets about the end of their last adventure, Rosalita, the Walshs' maid, discovers that Mikey's marble bag contains a large handful of jewels taken from the ship. Mikey's father quickly estimates that its value is more than enough to save everyone's homes. As the families celebrate, they spot the unmanned Inferno, now free of the cave, sailing away.