The natural world is full of colours. For us, they are a source of beauty, but for animals they are a tool for survival. David Attenborough reveals the extraordinary ways in which animals use colour: to win a mate, to fight off rivals and to warn enemies. New camera technologies - some developed especially for this series – also allow us to see colours and patterns usually invisible to human eyes.
Ultraviolet cameras reveal bright signals on a butterfly’s wings and facial markings on yellow damselfish that are used as secret communication channels. Some animals can also detect polarized light, and specialist cameras can now show us how fiddler crabs see the world, and how mantis shrimp have strange polarization patterns on their bodies to signal to a mate or rival.

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.

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).

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.

The tropical Indian Ocean is home to the Spice Islands. Characterised by beautiful sandy beaches, fringing coral reefs and coastal mangrove forests, this is a vibrant nursery area for marine life, such as whale sharks, crabs, seahorses and a great variety of fish. The coastal areas are where humans have the most direct impact on the ocean's resources.

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.