Ardos saves the main character's sister from Zook at the beginning of the game in Gateon Port, when he, Mr. Verich, and Eldes pass by to see him attacking the main character. In Citadark Isle, he reveals that he only saved the player so that the Shadow Pokémon plan would not be exposed to the world. He battles Michael on the Isle, but loses. After Greevil's defeat, he tries to convince his father to blow up the island and flee it; however, Eldes, to Ardos's dismay, convinces his father that they should all simply turn themselves in.
Ardos is extremely loyal to Cipher's cause, even telling Eldes that their father shall be referred to as the "Grand Master". He also shows far less in terms of morals than any other member of Cipher, even Greevil, as he tries to force his father to destroy Citadark Isle to save Cipher despite the countless deaths that would result instead of accepting defeat. Ardos somehow ends up avoiding arrest following his father's defeat, and can be battled in the sixth round of the Orre Colosseum. He explains to Michael that he fully intends to revive Cipher and, after that, he will declare Michael Cipher's biggest enemy and have Cipher constantly watch him.
"It's been a while, boy. Do you remember me? Do you recall this? I helped you in Gateon Port. …There's no need for thanks. I was merely punishing a fool that used a Shadow Pokémon in public. At the time, we didn't want the world to know what we, Cipher, were planning. Back then, I thought you were just an ordinary child…"
"Little did I suspect that you would become Cipher's biggest and most damaging threat. That's enough talk. You have the skills and wherewithal to reach Citadark Isle. Let me see your abilities in full glory!"
If lost before
"I had expected you to do better, but you disappoint me. Your abilities are strictly limited. You are but a puny presence not worthy of battling. Be gone!"
"This is trouble… If something's not done…"
After being defeated
"I realize now that I should have crushed you much earlier. This is out of my hands now. I must defer you to Master Greevil himself. But, boy, don't think that this is over. I won't abandon my dreams!"
After player defeats Greevil
"W-what? This can't be!"
"Grrr… It's your fault! I won't forgive… There is no forgiving you!"
"Grand Master! We're done here! We should blow up Citadark Isle with the child still on it!"
"Grand Master, such things can be replaced! We must ensure our own survival! I've readied a helicopter for our escape. We've got to leave now."
"Ashamed? Clinging to foolish hope will guarantee Cipher's demise! Cipher must survive. That is our first duty. The Grand Master feels the same way."
"Silence! Cipher will live forever!"
"If only this child hadn't…"
"Grand Master! Please give the order to blow up Citadark Isle!"
"Don't call him Father! Call him the Grand Master!"
"Silence, silence, silence! Why aren't you showing some spine! We've come so far!"
"What? You again! How did you manage to find us here?!"
"Grunt! I loath to admit it, but you're strong!"
"In all of Orre, I've never seen a Pokémon Trainer of your caliber. You appear to be the biggest threat to Cipher. To make sure my underlings watch you with caution, I give you the title “Cipher's Biggest Enemy.” From now on, Cipher's battle crews will be constantly tracking you. Watch yourself.