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Atlantis: Refuge is the second series of Atlantis. It's about rebuilding the City of Atlantis after a major Cataclysm.
After exploring the Underwater City and taking rest in it for a week, a major Cataclysm occurred. A bigger team of Divers, known as Zoo Xs 2, after finding out about the creatures the Deep Sea Salvage Crew found, the leader, Leo, CEO of Zoo Xs 2, thought about the money they'd make when people saw these animals. After estimating how much, he hired his group of 30+ Divers to go down into the Atlantic.
When down there, he captured all the creatures ad put them into captivity. He captured as many of the angry warriors as he needed and tranquilized them. The others he made flee.
After finding the Portal of Atlantis already opened, the team wondered what it would lead to. So they went through the portal on the Caterpillar Craft. Half of the craft got stuck on the other end, destroying the Portal, and causing the Cataclysm. Everything in Atlantis fell. The temple of Poseidon fell on top of Ace Speedmen, however, he wasn't crushed, instead, an opening in the temple saved him from being crushed. Sam got him out using the Torepodoes on the Wreck Raider.