The demo contained three songs: "Seed", "Shine", and "Dead of Jericho"; all three tracks later appeared on the band's first two studio albums.
In 1996, Gambina and Ramirez left the band, and were replaced by bassist Mike Bear and drummer Pat Magrath.
The following year, bassist Kirk Scherer replaced Bear in the band, completing the line-up that has lasted nearly a decade.
Ramirez recorded majority of the drum tracks for the album, while Magrath returned to play on the song "Heart Machine".
However, due to Ritter's commitments with Warbringer, the band re-enlisted Pat Magrath in 2009, and began working on their third studio album later that year.
In late 2014, Lum recorded himself playing guitar solos from several of the band's songs and posted the videos on Prototype's official YouTube channel.
However, on the band's third album, Catalyst, the band expanded from their earlier progressive metal sound to a more thrash metal-inspired sound, with aggressive guitar riffs, deeper vocals, complex bass lines and fast drum patterns and blast beats.