Hmm. Sounds apocryphal. By Executive Order 12333[1] the CIA is legally prohibited from collecting intelligence inside the United States in the vast majority of situations. The CIA cooperates with the FBI in these cases. Hypothetically this could be some kind of base for foreign intelligence operations, but that seems unlikely considering that I can't find any supporting evidence for the event occurring with some basic Google searches.
Edit: Let's be clear here: yes, there are a million hypothetical reasons why this story might actually be true. Unless someone can find a reliable source that confirms any of the details in this article I'm going to remain skeptical.
While the CIA is prohibited from intelligence gathering activities within US shores, this doesn't mean they're prohibited from opening an office for any other activity.
The CIA is quite active in the tech world. For example, they underwrite a venture capital firm (http://www.iqt.org/). There are many other quasi government companies active in the tech world throughout the US as well. Most of them don't hang up a billboard with exactly what they're up to, for both obvious reasons as well as the same PR behaviors that govern all companies (for better or worse).
Before you break out the tin foil, consider that it's quite reasonable for an organization like the CIA to be interested in tapping into and recruiting from the sort of uniquely high expertise pool that forms around institutions like MIT.
While I think concerns about oversight and ensuring rights are preserved are entirely reasonable, if the CIA weren't this active domestically, I think it'd warrant a call to your senator to demand more from your government.
As I read it, the story sounds _exactly_ like the kind of thing I'd make up if I were the CIA and wanted to convince anyone that I didn't have an office in the area.
It would nicely convince everyone that I was not present, I was unlikely to return because I had been resoundingly bested, and if I were to return, I would be so ham-fistedly obvious that I would be easily detected and so anything less obvious clearly couldn't be me. It'd be perfect.
I suppose if I wanted to take it one level further I'd actually even make it real and have it play out as a script. I'd set up my real office somewhere opposite and unobtrusive and watch the fun.
That said I agree with the other comments. I'm not really sure what the point of setting up an obvious office would be outside of the already mentioned recruiting or academic interactions which seem to have little need to be covert.
Because of the last paragraph of this seriously bogus article. The banner was indeed posted and then a nice guy from the CIA office went across the hall and pointed out that while access from the central section with the elevators was controlled (with a Medco lock in the case of MIT's space, not that it was that difficult to get a copy of it), the bathrooms had no such protection, you only had to get past the guard on the ground floor and sign in (a necessary precaution due to the very bad neighborhood Tech Sq. was next to).
So that given that there are people out there who really hate the CIA, if someone were plant a bomb in one of the bathrooms it might very well be an MIT person who "found" it. The banner (in LOGO lab space?) was immediately taken down.
The CIA did not leave; they told MIT they'd be happy to if MIT would pay for replacing their built into the structure safe, which MIT was never willing to do.
seems like a good match if you want to recruit people who are into secrecy. if you want to recruit potential spies, you don't want your foreign intelligence agencies noticing who you are recruiting, do you?
If foreign agents are moving with impunity in the US and watching recruitment operations without anyone knowing I think the CIA/FBI has a bigger problem than recruitment.
Anyway, this still doesn't explain why I can't find another source that supports this article.
[1] https://www.cia.gov/about-cia/eo12333.html
Edit: Let's be clear here: yes, there are a million hypothetical reasons why this story might actually be true. Unless someone can find a reliable source that confirms any of the details in this article I'm going to remain skeptical.