Naps's first appearance is at the Pokémon HQ Lab, where he, together with two other Cipher Peons, attempts to kidnap Professor Krane. With Krane's guidance, the playersnags Naps's ShadowTeddiursa. Naps and the other two Peons then escape in a truck with Krane, bound for the Cipher Lab. In this battle, his Trainer class is Spy rather than Cipher Peon, due to his affiliation with Cipher being unknown at this point. He is one of the few Trainers in Orre to ever fight in a Single Battle.
The player then runs into Naps at Cipher Lab, where Professor Krane is trying to convince him to leave Cipher. The player battles him in order to save Krane. After that, he tells Krane that he is still loyal to Cipher no matter what Krane says to him, and runs off, never to be seen again.
"You can't be serious. Listen to the man already! He's been saying all along that he won't help our Shadow Pokémon plan…"
"Being off by just a little tiny bit is enough to make it drop a ship? And would you look at the uproar…"
"You put a lid on it! When it comes right down to it, it's so all your fault. Come on, help us with XD001!"
"…Prof. Krane. I understand what's you're trying to say, but I can't help you."
"Whoa?! You… Aren't you that kid I saw at the Pokémon HQ Lab that time?"
"Are you trying to tell me that you came here by your lonesome to rescue Prof. Krane?"
"It's too bad, I'm still a member of Cipher. I can't very well let you folks go now, can I?"
"As for you… You snagged my Teddiursa from me that time! I'll give you this. You've got guts to come here alone. But I'll fix you good so you'll never get out again!"
"You're good, punk…"
After being defeated
"Prof. Krane, you folks don't have the foggiest notion about how big and scary Cipher is. It's not smart to resist. You can go on about the poor abused Pokémon and all, but you should think about your own selves. That's my advice."
When battling Naps's Teddiursa at the Pokémon HQ Lab, the player is given no choice other than tossing a Poké Ball, which will always succeed. Normally, the chance of catching a full-health Teddiursa with a regular Poké Ball is only 15.6%. If the player deposits or tosses all their Poké Balls prior to the battle, an extra one will be placed in the player's inventory.
Unlike most Trainers within Pokémon XD, Naps is aware when Michael snags his Shadow Teddiursa, likely because the snag is required to advance the plot. Casual Guy Cyle in Gateon Port will notice if the player snags his Ledyba, and Greevil will also notice if the player snags his Shadow Lugia.