I was envisioning the story taking place around season 2 of Arrow. As far as Chuck goes, he's had the latest intersect in his head for over two years so while the combat skills are still good, the info is two years old.
I'm not sure if any of Oliver's information about his time in Hong Kong would be in the intersect because A.R.G.U.S. isn't apart of the CIA or NSA so that might be a good reason that Chuck won't flash on Oliver.
Felicity might be looking to see if any of the alphabet agencies have any information on (take you pick on villians). She happens to have the bad luck to hack into the CIA servers while Chuck (working as a consultant) is busy upgrading the system/firewalls/doing-his-own-hacking.
This causes a digital game of cat and mouse between Chuck and Felicity who bring in their respective teams into the game. Team Chuck is tasked to find the hackers while Team Arrow is, under Felicity's direction, leaving false physical trails to match Felicity's digital trails.
If I think of anything else for this challenge, I'll post it up.