AGRA are the people after Mary who want to hurt her.
The flash drive contains false information.
Jim made the flash drive and the lies on it.
The punctuation is a clue.
In the season three DVD commentaries, Steven Moffat said that what was actually on the flash drive was five episodes of Doctor Who. While this is obviously false, the fact that he brought it up at all - and said what was on it - probably means that the narrative isn’t done with the flash drive and Moffat thinks you should be curious as to what’s on it. There’s definitely more to the flash drive than the obvious.
So what the hell could be on that flash drive … and what the hell is AGRA?
First off, I don't think AGRA is Mary’s initials:
Mary puts the flash drive on the table; Sherlock immediately asks about AGRA:
Mary looks a bit deer-in-the-headlights, which is very much not her:
Then, for the only time in the whole conversation - the only time in the whole season - Mary hesitates and stutters over her words:
She’s lying. AGRA aren’t her initials, and what’s more, Sherlock knows it:
He purses his mouth and looks away. She’s lying and he knows it.