The black marker was the original Marker found on Earth. Spawned from that Marker by scientists was the red marker (along with many others, that were never truly finished, which happened LONG before Issacs time). soon after that, they found out that it brought dementia and the horrors of the Necromorphs, where upon it was sent to Aegis 7 and the planet was marked to be Forbidden.
In an illegal mining operationt the USG Ishimura cracked open Aegis 7 and red marker. the effects of the red marker took effect, but someone (her name, I forgot it) sent out an SOS beacon. Due to his girlfriend being the senior medical officer onboard the Ishimura he voluntered to be the engineer for the rescue operation, and ergo Dead Space. Dead Space 2, Issac was captured by Unitologists and moved to the station orbiting Saturns moon, Titan. On that station he was drugged and used over a span of 2 years. Issac Clarke and Nolan Stross (who was the lead scientist on the operation to figure out what happened on Aegis 7, and was 'touched' by the red marker and found Issac Clarke) built the Yellow Marker.