Right after Junpei went through door 3 in the infirmary...
Junpei: Damnit, I lost her!
He took a step toward the stairs, muttering angrily to himself--
Then suddenly, Junpei felt a sharp pain in his neck.
As if he'd been stabbed by a needle, or...
He tried to spin around, but his body refused to respond.
The attempt at movement was enough to disrupt his balance, however, and he staggered and fell, tumbling down the stairs to a landing.
Or rather, into a pool of water several feet deep that had gathered above the landing.
He felt his body begin to sink.
Straining to keep his head above water, Junpei finally saw her.
Clover.
She was reaching out for him with her left hand, an eerie smile frozen on her face.
Clover: Here, take my hand...
Junpei: Clover...
Junpei: What... what did you...
Clover: Just a little injection. That stuff Ace took? I got some from his pocket.
Junpei: There... there was more...?
Clover: Mm-hm.
Junpei opened his mouth to try and ask why...
But there was no point.
He already knew.
Junpei had left Clover and Lotus, and gone through door [3].
The body on the other side of that door had been Snake's.
Clover likely thought Junpei had killed him. It wasn't a difficult jump to make.
...Or perhaps losing her brother had simply driven her insane.
The cold, vacant look in her eyes would have made Junpei shiver, if he wasn't already paralyzed and about to die.
Clover: What are you doing? Hurry up and grab my hand.
The injection she'd given him seemed to have worked its way to Junpei's brain.
Thinking was becoming increasingly difficult, and everything felt... indistinct.
Clover: You idiot! Why would I help you?!
The last thing he heard was the soft gurgle of water as his face dropped beneath the surface.
As he sank, he could see Clover's face getting further and further away.
The water twisted and distorted it into something that barely seemed human.