1999 is the year in the sixth Matrix that Neo was freed, first visited The Oracle, then survived being killed by Agent Smith after freeing Morpheus from interrogation. The seventh Matrix was stuck on the year 1999, with time being reset every New Years to the beginning of 1999. The date in the Real World, however, is many years beyond this.
After watching Neo in 1998, the crew of the Nebuchadnezzar approached him and in 1999 gave him the choice to learn the true nature of the Matrix. He was freed, and taken to visit The Oracle, who told him that he was not The One. On their way back, Cypher had betrayed their location, and police and Agents closed in on their position. Morpheus allowed himself to be captured in order to give the others time to escape, but Neo and Trinity went straight back in to free him from interrogation. After rescuing Morpheus Neo was shot dead by Agent Smith, but was revived by Trinity in the real world; returned to life, Neo realised his power as The One, and seemingly destroyed Smith.
On September 18, Neo returned to the Matrix to give the Machines a message: he could sense their fear and would show the people in the Matrix a world without rules or controls. After hanging up the phone, Neo proceeded to fly away. In the final three months of the year and the first three of the next more potentials were freed than in the previous six years, which Morpheus told the Council was proof that the Prophecy would soon be fulfilled.
The Omega Hardware Solutions OHS-T1 personal computer was also produced during the year.
In a conversation with SiskoUrso in Maribeau, the exiled program Tick Tock said that at the moment of New Years each year, time was reset in the Matrix to 1999, to keep technology at the same level in the Matrix.
- The film was released in 1999, so when Morpheus challenged Neo's belief in the year during the film, it was also addressed to the original audience, challenging their preconceived ideas.
- The Matrix starts off with a call log between Trinity and Cypher in 1998, while the crew of the Nebuchadnezzar are watching Neo, and ends with a call log between Neo and the Machines in 1999.
- Morpheus says to Neo after freeing him that while he believes the year is 1999, the real date is closer to 2199. In fact, as their Matrix wasn't the first Matrix, the date was several centuries later than either figure.