It was a nefarious program, created from leftover Cyberman technology, which itself led to the creation of a computer virus that became known as the Codex. When activated, the program would warp reality as if by magic in an attempt to harness the power of Saraquazel, an ethereal sentient power from another Universe, which was fated to exist after the destruction of the current one.
The Codex was written in a language that few could understand: Quantum mnemonics, the language of the Great Old Ones. The Codex was apparently aimed at summoning Yog-Sothoth, also known as the Great Intelligence, to London, though a counter spell could be used to disrupt the summoning and thrust back Yog-Sothoth to its own universe. Quantum mnemonics represented the physical laws of the Universe that preceded the current one, Yog-Sothoth's own, and were capable of rewriting reality on the most fundamental of levels. Their use and interfering with a mnemonic were known to have unpredictable side effects.
Mel Bush, while travelling with the Sixth Doctor, was clandestinely given a copy of the Codex from Ashley Chapel Logistics by suspicious former employees, who believed Chapel intended to use the Codex in a massive banking system fraud, Mel hooked herself up to the company's mainframe, and using the TARDIS library as a reference point, tested and partly debugged the program. Ironically, her efforts to understand the Codex led to its completion and activation by Chapel.
The real aim of the Codex was the creation of a bubble of space-time which obeyed the physical laws of Saraquazel's universe, freeing him and bringing about a new age of peace and prosperity to the planet through Saraquazel's power. However, when the Codex was used, Anne Travers cast the counter spell, due to her great fear of the Great Intelligence; this resulted in the merger of the physics of this universe, the Pre-Universe and the After-Universe. Reality changes around London created the Great Kingdom, an unstable domain with contradictory laws of physics, ruling over both technology and magic, which would eventually tear it apart. Three gods existed in the new world: Saraquazel, Yog-Sothoth and Lady TARDIS, though the two became merged into a single, insane entity as a result of the backlash of power.
The Great Kingdom consisted of three regions which were the Ziggurat, ruled by Technomancer Melaphyre (the new reality's Millennium Hall, ruled over by the warped form of Melanie Bush), the Labyrinth, ruled by Hierophant Anastasia (the remains of the Library of St John the Beheaded, led by the changed Anne Travers), and the Tower of Abraxas, lorded over by Archmage Ashmel (the office building of Ashley Chapel Logistics, still dominated by the new Chapel himself). The only way to restore the normal world and shatter the bubble was by forming a chain of cybrids between the key structures of each domain to short out the connection between the Universes. The one who headed the chain that completed the link, however, would face the release of power, an event likely to kill the participant. (PROSE: Millennial Rites)