Mycroft Holmes: I have access to the top level of the MI5 archive.
Mary Morstan: [already looking at that archive via her phone] Yep, that's where I'm looking.
Mycroft Holmes: What do you think of MI5 security?
Mary Morstan: I think it would be a good idea.
I don't know exactly what the last line of Mary Morstan means.
Also, in that sentence, what does "it" refer to?
Best Answer
What Mycroft means is
Mary understands the question, but she believes that materials at MI5 are not really protected very well. She may even think that the protection from espionage at MI5 is so poor that there's "no security" at all.
The meaning of her reply is:
She is being sarcastic with this answer. She subverts the meaning of Mycroft's question in order to express her disdain regarding the abysmal level of security at MI5.
She reframes Mycroft's question as if it meant:
It in her answer means "setting up a security system".