When they eventually make it past Basic Training, they've gone from 30 recruits to roughly 16 Junior Agents.
Penny and Nathan are both among those.
There's a weird guy in the room with them, though, and that takes priority at the moment. He has shimmering (yes, shimmering) eyeglasses on, and when he drops (drops?) the pen (pen?) he's holding, that's when everything goes to shit.
An electric pulse ripples out to the walls of the blindingly white room, and suddenly the soles of their shoes are melting and they're forced to step out of them, bare feet on the tiled floor (some part of Penny's mind keeps telling her that it's easier to clean blood off of tile).
"I'm Precedence." The weird guy says, eyeglasses still doing the odd shiny-glowing thing. "In a moment, we'll be seeing how that foreign pulse affects your bodies."
And suddenly, there's excruciating pain in Penny's forehead, and her sight goes all wibbly-wobbly and it's all screwed up and she can't breathe and her sight is going cross and-
Aaaand that's when she realizes she now has a third eye right smack-dab in the middle of her forehead. Fabulous. There will he words with the director later.
Nathan, meanwhile, is having some trouble too. Numbness has flushed down his arms, twirling bright blue patterns on his skin, embedding themselves. It kind of hurts, actually. He can feel them crawling down his back, too, and running up from his ankles. One creeps up to the edge of his jaw and stops there.
They're florescent. The hell is this his life.
But then there's an authority figure bursting through the door to the room, shouting "DAMMIT PRECEDENCE I TOLD YOU YOU COULDN'T EXPERIMENT ON THIS BATCH OF JUNIOR AGENTS YOU WERE SUPPOSED TO GET THE REJECTS."