Marcus orchestrated his father accidentally taking the MI-5
Marcus made sure that his father would end up taking the entrance test for MI-5
instead of for the low level civil servant. He already knew his father was capable of more and is just pushing him. It's all a master plan to establish a connection in the secret service.
There is no Marcus, Judith, Philip, etc
Everyone is part of the delusional fantasies of Tim, a homeless man. Possibly of a very mentally disturbed computer store technician, Chris.
Tim's boss is not crazy or incompetent
He has meant to do everything that he has done, including putting that throwing star into one of his employees.
Philip will try to leave Judith and she will lose her mind
Philip will end up trying to leave Judith and she will flip out, blaming Tim for everything. Also Philip will somehow manage to move in with Tim during the time that he is separated from Judith.
Marcus is an extension of Cthulhu
Marcus is actually a small piece of the old one, Cthulhu, extended into the Spy Universe specifically to torment Tim who is the reincarnation of the last wizard to banish Cthulhu to the far reaches of the Universe.