If you asked Akinari the whereabouts of the pen, he will say a creature with white fur and red eyes took it. Go to Koromaru in the dorm (after he's joined) to get the pen. --- We are all chained - chained to our own secrets and the persona we wear to hide it.
I have a problem too, I'm sure I talked to the guy and he mentioned his pen getting taken away, but when I talk to Koromaru in the dorm, it won't give me the pen --- You may have the better car, but i'm a better driver
Then on a Sunday go to Naganiki Shrine and go to the bench at the lower left corner and talk to that skinny dude and if your academics is high enough you will get to pick from three choices (not sure if the choices matter but i always pick "almost zero").
And after that he will mention his pen.
So go do whatever. Then when you get back to the dorm in the evening talk to koromaru and choose to pick up the pen when given the option.
--- Not changing this until people start realizing that reality TV syndrome is a poison!