Despite having "died" during the course of the third film, Trinity made a return to the series in the official continuation, The Matrix Online. Taking on a major role in the game's final chapters it was revealed both she and Neo were actually the cumulation of decades of Machine research into translating human DNA perfectly into Machine code, allowing them to interface directly with technology without the need for simulated interfaces.
Originally developed by the Oracle, this program was called The Biological Interface Program and was strongly sought after by the Oligarchy as a means to transfer their digital minds to physical bodies instead of the mechanical androids they had developed.
Without a physical form (the Machines recovered her program from her dying body) Trinity takes the appearance of a floating figure made of golden code within The Matrix. Initially distraught with her condition (confusion, anger and sadness being the prominent emotions expressed during her awakening after being freed from the Oligarch Network), she eventually finds solace in the fact her existence is the key to finally rebooting the Matrix and erasing Oligarch override control once and for all.
She ultimately meets her end in the Source of The Matrix, merging with a human inside the core of the Machine code base itself, combining the three core groups; Man, Machine and Program. This initializes the final reboot sequence, removing the Oligarch control and allowing the Machines to finally exist without fear of cruel masters. Although it is unclear from the outlines Ben Chamberlain released prior to the game's closure, this conclusion likely sees the creation of a new truce between Zion and The Machines and is the basis for the new Matrix created around the concept of human thought control.