Cipher

"Ah, you've finally reached me. I must say that I am impressed. I welcome you to Aether Tower. My name is Cipher. Do you remember? The time that we met in Forretree Village? I did have the feeling that I would one day face you in battle... But I never imaged that you would be the one to seek me out here. Very soon, we will be ready to greet your arrival in style. I will go ahead and wait for you. Don't keep me waiting too long."

Description
Cipher is the primary antagonist of Pokepuff version 2 and the leader of Team Shadow. He is a man with an intimidating physical stature. He is gaunt, dressed in dark purple clothes, and has wiry serpentine hair. He could have some connection to the supernatural, as he can often disappear into shadow, leaving behind visions of his glowing red eyes. Often described as a man of pure evil, he is truly a malicious character, caring nothing about the welfare and safety of his Pokemon or his friends and acquaintances and willing to give them up if it means saving himself.

Role
Cipher is the creator of Team Shadow's' plan to build an army of Shadow Pokemon and steals a scientist named Aristotle's invention, the snag machine in order to carry out this plan. Later, he enlists the help of Team Rainbow Rocket, another criminal organization, as a front for Team Shadow's plan. (Unbeknownst to Cipher, Giovanni and Team Rainbow Rocket had their own plan to build an army of Ultra Beasts.)

In the finding Snorlax quest, Cipher is in his mansion in Forretree city. He battles the player's Pokemon with his Combusken. After being defeated, Cipher reveals that he is using the snag machine to artificially "shut the doors" to the Pokemon's hearts. He then mysteriously disappears.

In Chromium city, he will battle the player at Aether Foundation's international headquarters, where he holds Lusamine prisoner. This is the first battle in which he uses his Metagross. He will defeat the player using Shadow Moves and disappear again.

In Team Shadow's headquarters, it is revealed that he holds Ho-Oh Captive. Because the snag machine does not have enough charge to convert it into a Shadow Pokemon, he tries to train it as if it was his own Pokemon. When it refuses to show loyalty to him, he punishes it by shocking it with electricity.

After being defeated by the player, Cipher abandons all of his Pokemon and attempts to flee in a helicopter. A few seconds after Cipher's helicopter takes off, Ho-Oh breaks free and attacks the helicopter with Sacred Fire, destroying the helicopter and presumably killing Cipher.

Trivia

 * He is based on Nascour from Pokemon Colosseum
 * He is the only character in the game to have more than two Shadow Pokemon.