With all the talk of who the villian is I am surprised most people havnt thought maybe john harrison is a operative of section 31. Heres some of the reasons I think it is section 31. first of all in the last page of the newest recently released cowntown into darkness comic book apirl uses a code to give him control of the enterprise and the code is EMERGENCY PROTOLCOL 31. Also in the comic pike tells kirk to just forget about everything that happend and it is revealed that harrison has access to top starfleet access codes. Also in the international trailer Marcus says it was done by one of are top agents. Lastly wasnt there a section 31 operative by the name of harris who was in a episode of enterprise? I may be thinking to much into this but one thing is for sure harrison is a member of starfleet which is part of section 31.
A nice thought and the comic is definitely making a nod to it, but as far as in the movie? Doubt it will be any more of a mention than that of "Admiral Archer's prize beagle" was in the first.
They were also trying to recruit Sulu in the Ongoing comic (Return of the Archons). I've been convinced that STID will be about Section 31 eversince.
You obviously haven't been looking in the right threads. The IDW Ongoing comic dropped easter eggs (or red herrings) about a group that may or may not be Section 31 way back during the "Return of the Archons" storyline.
Admiral Marcus calls John Harrison "one of our top agents" in the last trailer, which screams Starfleet Intelligence to me, not the rogue group Section 31. They wouldn't answer to Starfleet or their commander.
Section 31 seemed to remain an extremely covert organisation in the Prime Universe for centuries. Perhaps they've become a bit more widely known about, having been exposed sometime after Nero arrived. Bound to be some knock-on consequences which have altered that version of the 23rd Century, which can explain Starfleet openly working with their own little CIA.
"Starfleet's CIA" would be Starfleet Intelligence. Section 31 is a criminal organization. If Harrison is indeed one of the best agents Marcus speaks of, than he'd be Starfleet Intelligence. Although, I guess there's no reason he can't be both...
The thing in the trailer referring to "one of our top agents" about the London explosion is something I don't think refers to Harrison. I think it refers to that guy with the little girl.. who was somehow recruited to do acts of terrorism by Harrison in return for helping his daughter. and that father was a top agent.
^^I think the first 38 minutes screened in Brazil does make it clear the "top agent" line is about Harrison.