Na versão estendida, os alienígenas estão causando o tsunami que poderia ter matado muitos humanos inocentes no litoral. Somente quando eles percebem que Virgil sacrificou sua vida para "salvá-los", eles mudam de idéia.
Nas FAQs no IMDB você pode ler:
"A very elaborate ending was indeed scripted and filmed for the theatrical version of The Abyss. It starts off after Bud is saved by the aliens. They show him the news on a giant video wall about the imminent war between the USA and the Soviet Union. This changes into a special report about giant tidal waves that appear everywhere around the globe, threatening all mankind. Bud instantly understands that the aliens are responsible for these tsunamis, and he asks why they want to destroy mankind. They respond by showing him images of the many wars and atrocities committed by humans in their seemingly never-ending route to self-destruction. But, as the waves are about to hit the land, they stop and retreat; the aliens have stopped them. Bud's sacrifice has showed them that humanity may have the strength and wisdom to make it after all. The movie then ends with the spaceship rising up towards the ocean surface."
Assim, ter um sub-número de militares estontoticamente obtusos de guerra vai para baixo porque eles tentaram rastrear (e possivelmente atacar) um de seus navios está em linha com seu "plano".
O plano é, eu acho: "vamos matar todos eles antes que eles matem uns aos outros".
Brincadeiras à parte, o pensamento alienígena pode estar aberto a grandes especulações. Como: eles estavam tentando alertar os EUA e a URSS, matando algumas centenas de milhares de pessoas, a fim de salvar centenas de milhões de uma guerra nuclear; ou, eles queriam o oceano para si e não queriam compartilhar o planeta com uma espécie de belicismo sem esperança. Da discussão sobre o filme emerge que:
According to the novelization, they were planning on exterminating us for the good of the planet. We were looked on as an out-of-control species that threatened all life on the planet. They decided to have some final up-close studies of Humans before they went ahead and that's when they had their close encounters with the crew of the Benthic Explorer, with Bud's deactivation of the nuke as final proof to them that we weren't all crazy and deserved a second chance.
A razão da vida real parece ser que o sub-afundamento está de acordo com o enredo original, mas torna-se difícil de explicar quando eles cortam a cena do tsunami por uma questão de comprimento.