Computer programmer Thomas Anderson, known by his hacking alias " Neo", is puzzled by repeated online encounters with the phrase "the Matrix" . Trinity contacts him and tells him a man named Morpheus has the answers Neo seeks. A team of Agents and police, led by Agent Smith, arrives at Neo's workplace in search of him. Though Morpheus attempts to guide Neo to safety, Neo surrenders rather than risk a dangerous escape. The Agents offer to erase Neo's criminal record in exchange for his help with locating Morpheus, who they claim is a terrorist. When Neo refuses to cooperate, they fuse his mouth shut, pin him down, and implant a robotic "bug" in his abdomen. Neo wakes up from what he believes to be a nightmare. Soon after, Neo is taken by Trinity to meet Morpheus, and she removes the bug from Neo.

Morpheus offers Neo a choice between two pills: red to reveal the truth about the Matrix, or blue to make Neo forget everything and return to his former life. Neo takes the red pill, and his reality begins to distort, awakening in a liquid-filled pod among countless other pods, containing other humans. He is then brought aboard Morpheus's flying ship, the Nebuchadnezzar.