SPOILER
No one knows what happened to the Black Marker as far as the audience of Dead Space knows. All we know is what happened in "Dead Space Martyr".
There are multiple black markers obviously because we know one was found on Earth and one was found on Tau Volantis by the Aliens. Both civilizations (humans and Aliens) were fascinated by it to the extent where they basically worshipped it and built replicas (red markers). The Aliens however were smart enough to finally realize the black marker would cause them to be eaten by the moon. Humans however have never realized this (except Michael Altman of course). Earthgov wanted to study the black marker because they knew it was an energy source, possibly infinite energy which is why they replicated the black marker like the Aliens.
As far as the Marker in Dead Space 2, that was another Red Marker such as the one found in Dead Space 1, and the one that is released near the beginning of Dead Space 3 by the Unitologist Leader when he blew up that building (which is what caused the necromorph outbreak there.
Now to enlighten you on something you may not understand, the Tau Volantis moon was a Necromorph, and there are more than just that one. The moon's entire goal is to become whole. Noone knows how, but the moon somehow creates a Black Marker and sends it down to the planet it is orbiting. It is knowlingly tricking the civilization into worshiping the marker and thinking it is good through telepathic signals to any Markers in range including red markers. It is all a part of "Convergence", where the humans evolve into necromorphs and eventually become one with the planetoid necromorph. Confusing I know but if you pay attention through all 3 games you really dont even need to read the comics or watch the movies.
