When Greg awakes in decommissioned Russian nuclear submarine K264's decompression chamber, he finds himself alone. All the crew are just piles of ash. Also, the computer produces a hologram of a young woman called Nedda. More sinister is that the air on the surface has become poisoned, there is no contact with anyone and it seems that he is alone in the world .
Shontel is stranded in a deep cave on Vancouver Island. On finding her way out she discovers that everyone is dead and encircling thunderclouds never go away. Contact is made with her and she is rescued, just before the clouds disperse and acid air surrounds her.
Nedda admits that she is more than just a computer hologram but an advanced life-form who can metamorphose into human form from her natural amoeba state. She arrived on the submarine to help Greg but was followed aboard by another of her species, a terrorist who believed that humans were a sub-species who should be exterminated. It attacks her but Greg and Shontel save her. She becomes a trusted friend as they travel through the ocean trying to find other human survivors and surface air that is not poisonous.
Later, they surface in the eye of a hurricane-type storm where the air is breathable and find a massive computer controlled tower but nothing alive. An elevator is discovered and they travel down to a vast underground cave of stalagmites. Here, they are met by a pony and small dog who led them to a wounded human named Lilad. He comes from an underground village of Cavair. A breakaway group, The Moss had attempted to kill him. Lilad tells them that is the youngest person in Cavair for no women have given birth for a generation. The Moss find their way to the surface and attempt to destroy the base. Their computer warns them and they escape in K264 before the base is blown up.
There are similar islands with access to Lilad's world. One has modern facilities that are not available in pre-industrial Cavair. Why is this so? There are two main buildings but one has been destroyed. Under it, they find an undamaged basement that contains a master computer that provides the fresh water and air to Cavair. However, the desalinised plant that feds in fresh water also has a sinister additive, a birth control chemical, hence the reason for no births for a generation. There are no records about who built the structure nor any reasons why births were being prevented but they disconnect it, anyway.
Problems are encountered in the cave when, on their way to Cavair they encounter a curtain of complete darkness where all light is neutralised. Apart from not being able to see, their progress through is not hindered. On the far side they make checks before heading out. This caution proves a lifesaver for they find themselves looking through a line of a hundred or more humans, including parents and children who are surrounded by a group of hostile men.
How is it that they arrive in exactly the right place and time to rescue these humans who are from Lilad's village? After rescuing the group, they are told that it is two years, not just weeks since Lilad disappeared. They had moved ahead in time! With the birth controlled water turned off, nearly all the women of child bearing years in the village are now pregnant or have children.
Opposing forces are striving to help or hinder them. Nedda suggests it is her kind responsible but since metamorphoses she has forgotten everything since meeting Greg.
In a final twist, they discover Nedda and Lilad's relation is the only person who can get them back to twenty-first century Earth but how is this possible?