The ending of Sea of Monsters restores Camp Half-Blood's barrier and brings Thalia back, then opens a new question about whom the prophecy means. Spoilers follow, and the reading below is my own opinion.
The mechanics are simple. Clarisse places the Golden Fleece on Thalia's tree, the tree heals, the barrier is restored and Thalia returns to life. Notice who does the placing: Mr. D handed the quest to Clarisse at the start, and the film lets her finish the job, even though Percy is the one the story follows.
The last twist is Percy's realization that the prophecy about a great hero might refer to Thalia rather than to him. In my opinion, that is the smartest thing the film does, because it answers the opening taunt that Percy is a one quest wonder. He spends the film carrying the weight of being the chosen one, and the ending suggests the label may belong to someone else.
It also leaves the bigger conflict with Kronos unresolved, since Percy locks the Titan away again rather than ending him. As such, the story reads as a middle chapter, and it could be argued that it was built to hand off to a third film. No third film was ever made. If you want to know what came next for these characters, the Disney+ series Percy Jackson and the Olympians is a television adaptation, not a film, and its third season, adapting The Titan's Curse, is dated to premiere on Disney+ on November 20, 2026, according to Disney's press site.