The novels in this trilogy are:
It is commonly assumed that the trilogy is chronologically placed in this sequence, however it is a matter of definitions or even taste as to which order they should actually be read or if it even matters. The time of writing or publishing is a bad guideline: all three novels derive from the same body of text to lesser or greater extent, and Burroughs continuously revised The Soft Machine and The Ticket That Exploded after their first publication, leaving only Nova Express untouched. Further, Burroughs use two techniques known as flash back and flash forward to fold in elements from later narrative into earlier narrative, and vice versa, making all events of the novels fall in all three books.
The trilogy is, because of its style, hard to decode or pin down in simple terms. This effect was probably also the intention of the author: one of the most prominent themes of the books is that language is literally a dangerous virus which must be battled with guerilla tactics involving delinearization of text as is exemplified by the cut-up and fold-in techniques.
The main story however quite clearly involves the view of a language virus as the source of several control mechanisms that keep humanity on this planet enslaved. The virus has several distinct personalities or attack paths which correspond to different persona of the Nova Mob. The virus/Mob is extraterrestrial and came to our world from the Crab Nebula which was the result of a supernova that occurred due to the Mob activities. Their first stop was however the planet Venus from where they attack Earth.
The goal of the Mob is to create so much conflict on earth that it will eventually explode in a supernova. This goal is close for the Mob when an intergalactical counterforce known as the Nova Police arrives. The Mob has actually been framed by one of its members: Izzy The Push. The Nova Police team up with other freedom fighters on Earth such as Hassan-i-Sabah and start fighting back.
The end of The Ticket That Exploded can be interpreted in two ways: either the Mob succeeds in creating a supernova of our planet, or they fail and get busted by the Nova Police, who destroys the language virus and replace it with total silence. Perhaps this is one and the same thing: both sides win.
The basic idea of language as a virus has been widely used and quoted from several of Burroughs' interviews. His own detailed account of this idea appears in the book-length essay The Electronic Revolution:
(The referred German Doktor Kurt Unruh von Steinplatz does not exist in reality and is another of Burroughs' inventions, possibly a word-play on the theologian Hans Urs von Balthasar.)
The essay then goes on to detail different counter-tactics for ridding the word virus. As pointed out by Burroughs himself, the virus idea shall not be understood as a metaphor but as the actual parasitic organism. It is unclear whether or to what extent he actually believed in this theory, but it has been suggested that it is structured in a style influenced by the controversial writings of Wilhelm Reich and L. Ron Hubbard, both of which are mentioned in the Nova Trilogy.
This theory underpins the three books of the Nova Trilogy and can be quite helpful to know when reading. For example in the last part of The Soft Machine unsuspecting primates are seemingly attacked by viruses falling from the sky, indicating its extraterrestrial origin.