Taking place partly on Earth and partly in the atmosphere of Jupiter, the story tells of Howard Falcon, the captain of a new and experimental giant-sized helium-filled airship. When an accident causes the ship to crash, Falcon is badly injured and takes over a year to fully recover. Whilst recovering , much of his body is replaced by prosthetics, converting him into a cyborg with greatly increased powers of speed, reactions etc.
In an effort to fully exploit his new powers, Falcon promotes an expedition to explore the atmosphere of Jupiter. Several years later, after many trials, the expedition is launched, with Falcon at the controls of the Kon-Tiki, a hot-hydrogen balloon-supported craft that descends through the upper atmosphere of Jupiter.
As the craft descends through the various cloud layers, Falcon discovers that the atmosphere supports at least two large forms of life, as well as microscopic and bioluminescent air plankton, producing atmospheric sea-fire. One form is a giant jellyfish-like creature (the Medusa of the title) about one mile across, and the others are manta ray-like creatures about a hundred yards wide that apparently prey on the Medusa.
The Medusa begins to show an interest in the Kon-Tiki, and for his own and the expedition's safety, Falcon ignites his emergency power and escapes back into the upper atmosphere.