I was thinking of a sidestory for season 5.Bryce was not the only guy who knew about the Intersect project.
Bryce’s old colleague,a former CIA agent, who was also enrolled into the Stanford CIA program at the start but went off the grid as this agent did’nt trust the CIA and was
misled by a Fulcrum agent and so he went rogue.This happened a year before Chuck came on the campus.
The backstory of this agent could be told in a secret file that Bryce left behind on Bryce’s computer as one his unfinished missions. This agent made contact with Bryce some
years ago wishing to defect to the CIA because he saw how corrupt the Fulcrum agency was from the inside.Instead Bryce told him to stay at Fulcrum to work as a double agent
and pass on Fulcrum secrets over to the CIA.
Bryce learns from the agent of the upgrades he had received as the Fulcrum agency knew from high scores on tests that this agent was capable of accepting an intersect.
This secret file loads up on a computer as new information on this agent is found and alerts the castle computer to warn Chuck of this spy who has a Fulcrum intersect which
is a unique version that is upgraded as well as he has nanobots inside him giving him some extra capabilities of Fulcrum design.
The agent could not make contact with Bryce for sometime and wondered what was going on.Bryce had been killed in the Intersect 2.0 room.The agent later tried to escape from
Fulcrum and make contact directly with the CIA and defect as he later on found out about Bryce’s death but did not make it in time as Fulcrum intercepted a communication at
the last moment implicating he was the mole leaking secrets to the CIA.The agent started suffering from his flashes and slowly with time became mentally unstable and is held
under Fulcrum security.He still is able to think clearly but at times cannot focus.
Chuck’s team tries to break the guy out as he poses a threat if Fulcrum brainwash him under mind control methods and becomes a mindless killing machine that can be controlled
through the use of the nanobots. Chuck gives this agent a regulator watch and with some luck the regulator works on the agent and his mind becomes clearer.The agent is
informed by Chuck of how they came to be there through that secret file and the agent trusts them to get him out.
Later on this agent fills Bryce’s position on the team and goes against the bad guys and is under training as an extra intersect.