Yeah, you are right, we have not seen Brandon Fletcher in the present time. Okay, so this is going to be a crazy long writing so bear with me as I expand on my theory of ‘who did it’.

I remember that after the bomb test in the episode 'Go', I found Brandon to be quite suspicious so I agree with your feeling on this issue. I highlighted in a theory previously that there had to be more than one mole in Quantico, so I theorize that it could be a team with the most likely ones being Shelby and Brandon. I wanted to include Simon too but I feel like he is a distraction from the discovery of the 'real' identities of the terrorist(s).

Of course, in order for this theory to work, there needs to be a proper backstory of Brandon in future plot developments to establish his 'troubled' past. Miranda Shaw mentioned in a past episode that "evidence lies, especially when it’s been put there on purpose". In the case of the presented ‘evidence’, we could see that Brandon might not a considerable ‘high’ suspect in the list but I assume that overlooking Brandon in future FBI investigations (as of episode 1x09) is purposeful (plot wise) in a way. I find this more suspicious as I believe that there could a combination of maintaining appearance (cover for status) and strong underlying motivations (something along the lines of a 'strong feeling' of being wronged, i.e: risk factors such as neglect, isolation, parental separation, early maladjustment, trauma from former military engagements, etc) that will drive the origins of his motivations and link them to the 'attacks'.

In the case of Shelby, we are meant to believe that her help in ‘financing’ her half-sister is the reason why she was so secretive to other Quantico recruit members (Alex and Caleb included). However, I think that is an elaborate ruse to distract us from linking the connection between the two moles. I believe that Shelby (undercover) could be working with Brandon in the present time within the confines of the FBI manhunt operation to find Alex, through giving out necessary information and new developments on Alex’s whereabouts to the ‘enemy’. To aid in her ‘undercover’ mission, she would have had to make the connection with Caleb and her ‘affair’ with Clayton to put herself at a psychological advantage (maintaining a lover/mistress façade - cover for action) whilst profiling the Haas family prior to entering Quantico. I believe that Clayton picks up on the inauthenticity of Shelby’s cover when he spoke to Caleb over the phone at the end of ‘Guilty’. Her motivations might be complex but I would highlight that it might be along the lines of the ‘injustice’ she experienced post 9/11. The stigmatisation of her parental loss would have been an immense burden and the lack of response from the government to prevent the event could be potential risk factors for her joining a shadow terrorist organisation.

Together, Shelby and Brandon could be a team of recruits from a shadow terrorist organisation (theoretically) that underwent special training for the purpose of infiltrating Quantico, whilst planning to frame Alex as the ‘terrorist’ from the very beginning. This would be achieved through deep undercover surveillance of Alex in class and outside of FBI activities, as well as post Quantico training period through analysis of psychological behaviours, life routines, activities, etc. The scale of this attack would require other background players that have not been introduced to participate in framing Alex. Nonetheless, I believe that Shelby is helping this organisation through funding (possibility but how?) whilst Brandon is secretly spying on Alex in class through discreet surveillance tactics. The problem now is the discrepancy in the narrative between when Alex was last seen prior to the bombing in Grand Central station and immediately after she was rescued in the pilot episode by the FBI. We need to identify any lapse in the ‘cover for status’ and ‘cover for action’ of these moles, so we can inspect on the incongruence of their explanations and their alibis. I will end my theory with a quote from Scott Stewart from STRATFOR who mentions the importance of paying attention to little details. He highlights that it “can be the difference between a potential attacker being identified and the attacker going unnoticed”.