Haruka is a delinquent student still struggling to graduate from high school after failing his exams before. The solution, according to Haruka's congressman father? Hire someone to make sure he gets into university by following him around and nagging him, of course! Shidou is supposed to be Haruka's "secretary" (read: babysitter), there to encourage him to pass his exams this time, but when Haruka only agrees to graduate on the condition that Shidou become his boyfriend... what's a megane character to do?!
Second Honey follows the rather unconventional relationship between the older, bespectacled professional Shidou and Haruka, the flippant student more interested in messing with Shidou and pissing off his father than actually pursuing his studies. Is Haruka just playing around, or is there really something there? Is this sweet feeling like real honey, or just a cheap imitation? Sometimes, even Haruka doesn't know.