Theory history: Submitted 2011-10-09, Doubtful 2014-04-06, Debunked 2016-01-15
For some reason, the player could reach the lighthouse, which is part of the core, as we know from the latest information. we also know that Murtaugh, after leaving the lighthouse, couldn't return to the core in a smooth way. So, if Murtaugh knew that the only way to regain access to the core was to destroy the subnet defenses in the edge, he left the messages in the lighthouse for anyone who could have reached it. he wanted us to experience with crystals of wisdom because they have a great power, and so he teleported away from the lighthouse. then he went back and forth trough the layers of subnet and the various "eras", leaving is messages for other people in order to use them for his purpose of revenge. then came the people and the scientists used by murtaugh to explore the net, but probably they died, because of the loss of memory and the defense systems. finally, the player, probably the chosen one, the only one who visited the lighthouse after murtaugh and einstein, took the wisdom gem from the basement and used it in the lighthouse, just after murtaugh left the lighthouse ( i assume that because the walls of the dungeon in the lighthouse are bright red) and then he travelled in time during the visit to the loop, the lab and the root. he then retrieved again the wisdom gem in the mission in the root, but in the future, because the place is the same, but with the walls with a consumed and aged colour. so murtaugh used the player to do a job in a place (the core) and in a time (before leaving the core) that he couldn't reach anymore to power the mover and reach the edge. the player deactivated the defense systems, probably created against mur, and Mur could do the mess that he did at the beginning of sub7 in the sanctuary.
Conclusion: Mur is a genius because he planned everything knowing he had the great risk that no one could take the wisdom gem and so do the "job in the past". Mur is freakin' insane, oh yeah.