James Cameron journeys to some of the Earth's deepest, most extreme and unknown environments in search of the strange and alien creatures that live there. Joining him is a team of young NASA scientists and marine biologists who consider how these life forms represent life we may one day find in outer space not only on distant planets orbiting distant stars, but also within our own solar system.
Aliens of the Deep is the result of expeditions to several hydrothermal vent sites in the Atlantic and the Pacific. These are violent volcanic regions where new planet is literally being born and where the interaction between ocean and molten rock creates plumes of super-heated, chemically-charged water that serve as oases for animals unlike anything ever discovered. Six-foot tall worms with blood-red plumes and no stomach, blind white crabs, and a biomass of shrimp capable of 'seeing' heat all compete to find just the right location in the flow of the super-heated, life-giving water or to fry.

On the coast, two worlds collide. Coasts are the most dynamic and challenging habitats in the ocean - that brings great rewards but also great danger. The extraordinary animals that live here must find ingenious ways to cope with two very different worlds. This episode is a rollercoaster ride of heart-stopping action and epic drama, peopled with characters from the beautiful to the bizarre. We meet fish that live on dry land and puffins that must travel 60 miles or more for a single meal, and witness a life-and-death struggle in a technicolour rock pool. In a secluded cove in the Galapagos, sea lions feast on 60kg tuna. It should be impossible - tuna are usually far too fast for sea lions to catch. But here the sea lions club together to herd their prey inshore. Once trapped in the shallows, these huge fish are easy pickings. As the tide recedes in Brazil, lightfoot crabs leap from rock to rock, desperately avoiding the water - their lives depend on it. Moray eels launch themselves from rock pools, jaw gaping. Then octopuses, too. Both crawl across dry rock to set their ambush. Elsewhere, the ever-changing tides create rock pools. But these temporary worlds are a battleground. Predatory starfish turn a magical garden into the stuff of nightmares.

This episode includes footage of wildlife inhabiting underwater kelp forests, thousands of giant cuttlefish spawning along a restricted area of rocky reef off the south coast of Australia. Males outnumber females 11 to one, which leads to fierce competition. Larger males use brute force to drive off competition, while their smaller rivals use deception by mimicking the appearance of females. The programme also features tiger sharks hunting for green turtles in fields of seagrass and spider crabs trying to avoid predators while they shed their shells.

Life goes to extraordinary lengths to survive this immense realm. A 30 tonne whale shark gorges on a school of fish and the unique overhead heli-gimbal camera reveals common dolphins rocketing at more than 30km an hour. Descending into the abyss, deep sea octopus fly with wings and vampire squid use bioluminescence to create an extraordinary colour display. The first ever time-lapse footage taken from 2,000m down captures eels, crabs and giant isopods eating a carcass, completely consuming it within three hours.

Sagan discusses the story of the Heike crab and artificial selection of crabs resembling samurai warriors, as an opening into a larger discussion of evolution through natural selection (and the pitfalls of intelligent design). Among the topics are the development of life on the Cosmic Calendar and the Cambrian explosion; the function of DNA in growth; genetic replication, repairs, and mutation; the common biochemistry of terrestrial organisms; the creation of the molecules of life in the Miller-Urey experiment; and speculation on alien life (such as life in Jupiter's clouds). In the Cosmos Update ten years later, Sagan remarks on RNA also controlling chemical reactions and reproducing itself and the different roles of comets (potentially carrying organic molecules or causing the Cretaceous–Paleogene extinction event).

In the third episode, a Velociraptor hunts pterosaurs on a cliffside by a waterfall. A battle-scarred Tyrannosaurus nurses his wounds and encounters a newcomer. With its feathered body and duck bill, the eight-ton Deinocheirus wades through an Asian wetland in search of relief from pesky biting flies.
A female Quetzalcoatlus builds and guards her nest. A mother Masiakasaurus and her family hunt crabs. Elasmosaurs enter an estuary in search of fish.