The ending says that the dinosaurs should be left alone, and it makes the point by letting the animals win the argument. The T. rex is sedated and locked back in the cargo hold, ending the city rampage. The dinosaurs are returned to Isla Sorna, and authorities declare the island a protected nature reserve.
Hammond appears on television to say that the animals should be left alone, which completes the mission he handed to Malcolm in the first act. The final scene shows the tyrannosaur family reunited on the island, with the idea that they can live undisturbed.
In my opinion, the interesting choice is Ludlow's death. He is killed by the animal he brought to the mainland, so the film punishes the plan to move dinosaurs rather than just the mistakes around it. Malcolm and Sarah solve the crisis by using the baby as bait to lure the adult back into the ship, which is a cleverer answer than force, and it pays off the moment in the jungle when Nick Van Owen freed the captured animals and the baby's parents tore through the team's trailers. The parents were the threat on Isla Sorna, and a parent's pull is what ends the threat in San Diego.
There is also a structural point I find easy to miss. Jurassic Park (1993) keeps its dinosaurs on an island the whole way through, so the harbor crash and the city rampage are the sequel's one big departure, a set piece that moves the monster to where the audience lives. Spielberg then spends the closing minutes sending it back, which tells you the film wants the city sequence to feel like a mistake being corrected rather than a new rulebook.
The reserve is also the most fragile promise in the saga. Jurassic Park III (2001) sends Alan Grant back to Isla Sorna anyway, in a film that runs 92 minutes against this one's 129, and by Jurassic World Dominion (2022) dinosaurs live all over the world. Jurassic World Rebirth (2025) then describes them as surviving mainly in zones near the equator. It could be argued that the protected island works as a closing image for this film, but the series never treats it as settled.