The Millennium Codex was a device created by Ashley Chapel, once right-hand man to Tobias Vaughn.
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 employees. David Harker, Chapel's chief of security, believed Chapel intended to use the Codex in a massive banking system fraud, and, wanting in, allowed her to hook to the company's mainframe. Using the TARDIS library as a reference point, Mel 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. (PROSE: Millennial Rites)