The needle injection was meant to create a telepathic link between Isaac and the Marker so that he can destroy it using his mind. However, what fake Nicole didn't tell him was that the link is two ways. So if the marker can destroys Isaac mind first, then Isaac will die in the real world. That's why if you lost during the final battle, you'll see Isaac killing himself with the javelin spear. However, if Isaac wins the mind battle against the Marker's mind/heart, then the Marker's physical body in real world is also destroyed.
You kinda have to sort out all of the dialogues/files you get throughout the game. Also, having seen Aftermath helps, I guess. Although technically, you should know by now that the Marker sends telepathic signals to those who come across it. What Stross and Isaac managed to create was a direct path to access the Marker's mind via the injection.