The Matrix is a ‘trans metaphor’, Lilly Wachowski says … The Matrix first hit screens in 1999, when Lilly says “the corporate world wasn’t ready” for an allegory - a story that can be interpreted to reveal a hidden meaning - about transgender people.

https://www.bbc.com/news/newsbeat-53692435

Here’s what one of the hormone pills used to transition looked like in the 90s:

https://i.imgur.com/PWHnOop.jpg

And some further reading:

https://en.wikipedia.org/wiki/The_Matrix#Transgender_themes