Despite its title, this song has nothing to do with the movie. Guitarist/vocalist Mark Jansen explained the track's meaning:
"The song is dealing about us humans, being caught in a matrix (an illusion) because of our excessive thinking. We have lost control over our lives and accept the illusion as 'the one reality.' But if we manage to free ourselves from those shackles and become masters of our thoughts again, we can make a huge step forward in collective consciousness and will be able to look beyond the borders of our matrix."
The track is one of Jansen's favorites on The Holographic Principle. He explained: "Musically, the song has quite a simple structure and the catchiest chorus, but the middle is completely wild. That's what I really like about it."
The song's visual was produced by Jens De Vos and his team at Panda Productions. Commented Epica frontwoman Simone Simons: "The energy that lives within 'Beyond the Matrix' is extremely contagious. It will sweep you off your feet when the melodies enter your mind. The video embodies the spirit and liveliness of Epica."