If you really wanted to have fun with this plot you could cast Trinity as a quack Paleontologist who believes an alien species existed on earth thousands of years ago. She succeeds in convincing Neo because, well, he’s got a huge crush on her, but also because he had a suspicious dream in which he is told to “follow the white rabbit” and guess what kind of tattoo Trinity has?
He decides to help her try to gain access to a dig site that has suspiciously attracted the attention of the Federal Government. Convinced of a cover-up, she and Neo slip into the cordoned off area and discover “alien” technological remains far more advanced than anything that exists at the time. Even more shocking, they discover what appears to be human remains; meaning, Neo and Trinity’s world had already gone through the process of polluting the planet, escaping into a Matrix, and being unplugged by some other Neo-like character. This is the first hint to the audience of the existence of multiple Matrixes.