John Brannigan was born in the 21st century, eventually becoming an Ultra and captain of the Nostalgia for Infinity. One of the most extremely modified Ultras, he was originally able to survive prolonged vacuum exposure without a suit. His augmentations were so advanced that the crew believed only Calvin Sylveste had the expertise to repair him, which he (or his beta-level) did on several occasions.
Falling victim to the melding plague, Brannigan was frozen near absolute zero in a reefersleep casket by Ilia Volyova to prevent the spread of the disease, which had begun to fuse him with the Infinity. Later he was forced to become more integrated with his ship, with the plague as the catalyst, and ultimately became one with it; afterwards he suffered erratic mood swings, even going so far as to attempt suicide with hell-class weapons.
Volyova found it is possible to converse with Brannigan by warming the core of his brain enough that other equipment could stimulate and read his mental activity. He was rarely lucid, and had little memory, but he provided Volyova with occasional companionship and insight during the fifteen year journey to Delta Pavonis. During the journey to Resurgam, then to Hades, it was revealed to the crew that Brannigan murdered his first officer, Sajaki. During a visit to the Pattern Juggler world of Wintersea, Brannigan had Sajaki's neural pattern overwritten by his own – erasing Sajaki and effectively creating a duplicate of himself, ensuring his survival even if he was unable to recover from the plague.
Volyova, on piecing together this crime, and requiring a force to counteract Sun Stealer's growing control over the ship, destroyed the medical equipment previously holding the plague at bay. The Melding Plague affected the captain by merging him with the ship, in such a way that he retained his own consciousness, and demonstrated increasing control over the ship and its weapons.
The Captain shed large parts of himself during his descent to Hela, where he intended to 'dock' with the planet and alter its orbit so that it rotated at exactly the same speed it orbited. Shortly after landing, Quaiche's soldiers infiltrated the Nostalgia for Infinity and began to eradicate his presence within the ship. Before he dies, however, he was able to activate one of his three on-board hypometric weapons and kill Grelier, who was holding Aura hostage.
- Brannigan is a very mysterious character, hovering between wisdom and abject madness. He does have a respect for Clavain and is (by Absolution Gap) the only other character who can compare with him in terms of age, wisdom and experience, although the captain stated that he was already an old man when Clavain was born. The Captain at one point projects an image of himself from his oldest memories, in which he appears as a normal human in a spacesuit that is hinted at being very similar to those used by NASA astronauts, suggesting he originates from approximately our own time.
- John Brannigan is possibly the oldest human character in the series, surviving from the near future to 2727.
- Throughout Redemption Ark and Absolution Gap, it is hinted that Captain Brannigan was responsible for many immoral acts in his very long, pre-plague life.
- The Melding Plague affected Brannigan in a different way to other descriptions of the Plague in the Revelation Space series. Why this is is unknown.