It's a story about this dude and his childhood friend along with this other girl for added drama. The childhood friend goes into a coma, yet Keisuke, the main character, is the only one who can see her ghost (and she's in pajamas; hence the title). Makura, the girl, can't remember what happened right before she "died", so the mystery and point of the series is to find a way to bring her back to normal.
And the other girl? She's helping out. Except she and the rest of the people in their school don't know Makura's in a coma for some reason. Predictably, A love triangle ensues; along with drama like jealousy at the beach, a kidnapping, and Keisuke getting stabbed in the chest by a dude with a knife.
It's also ecchi. Normally that's not a notable thing in itself; but dear god, this manga is just so creepy about it.