"I'm glad that it has gotten out that that was the original intention," she said. "But the world wasn't quite ready for it — the corporate world wasn’t ready for it."
"I'm glad that people are talking about the Matrix movies with a trans narrative; I love how meaningful those films are to trans people, and the way that they come up to me and say 'these movies saved my life.'"
"I'm grateful to be able to throw them a rope to help them on their journey," she added.
She said the themes of transformation, imagination and the seemingly impossible becoming possible all speak to the franchise's trans fans.
"The Matrix stuff was all about the desire for transformation — but it was all coming from a closeted point of view," she said.
When the film was released in 1999, both Lilly and Lana were pre-transition, known as directing duo the Wachowski Brothers.
Lilly confirmed that the character of the aptly named Switch, one of the Nebuchadnezzar crew members played by Belinda McClory, was originally meant to be male in the real world but female inside the Matrix: "That's both where our head spaces were," she laughed.
She admitted she didn't know how "present my trans-ness" was in the back of her brain while writing it; but "it all came from the same fire."
The Matrix tells the story of Neo, played by Keanu Reeves, a former computer programmer who learns the world he lives in is actually a computer program used to sate humans, who in the real world are obliviously used as bio-electric energy sources by a sentient race of machines who defeated them in a war.
It was followed by The Matrix Reloaded and The Matrix Revolutions, both released in 2003.
A fourth film, reuniting original stars Reeves, Carrie Anne Moss and Jada Pinkett Smith, as well as Lambert Wilson who playedThe Merovingian, is slated for a 2022 release.