Alya had been kept in the Cipher base for a few days. She had talked to a lot of Cipher members, and she was being treated much better than she had feared. Many Cipher members would come by and greet her, and most of them treated her with respect. She was being well fed, and she had been given a lot of books she could read. The downside was that she couldn't leave her room. But she got news from outside from many of her new aquaintances. One of them, Lipen, a Cipher peon, came by each day to talk to her and make sure she had what she needed. She figured that was his job, but she was happy about it. He had told her that her father had set up a largescale search for her, and that pretty much every trainer in Orre not involved with Cipher was helping out. He had also told her a little about their plans. They were the same as usual. Steal and capture some pokémon, turn them into Shadow pokémon, use the Shadow pokémon to gain money and steal more pokémon. She wondered why they kept trying. She knew that someone would come and thwart their plans, or that the government would get it done.
Then Lipen came into the room. He had a more serious expression on his face this time. "What's wrong?", she asked. "You have to come with me." he replied. She wondered what was going on, but didn't get to think too much about it, as Lipen hurried her out of the room. They were walking to their destination, and it was apparently a fairly long way, to be inside a building. She couldn't get Lipen to say a word to her as they walked. She decided to take a look around instead, to see if there was an exit.
She was in a bright grey hallway, the usual Cipher ornament. The walls had several weird shapes; instead of being straight walls, they seemed to be thicker at some parts than at others. There were no windows, and nothing to look at. A peon walked past them in a hurry. Alya and Lipen kept walking. Since there was nothing worth noticing along their route, Alya attempted memorizing the turns they had taken, to see where she'd end up in relation to her room. It was a long walk, however, and she eventually lost track. Another peon walked past them. Alya shifted her thoughts over to why she was being taken to wherever she was being taken. She couldn't think of a reason they'd need her, and if she had inadvertently picked up something, they'd have taken it earlier. She didn't have much more time to think, though. Lipen stopped, and put a hand on her shoulder. To her right was a door, like many they'd passed. They were apparently going into this one, though. Lipen didn't say a word, but stood still. The door opened up. He told her to walk, the first thing he had said to her since they left her room. She entered the room. Cautiously at first, but she realized that there was nothing dangerous, and picked up her pace a bit. Eventually, they reached a man in a white coat standing by a computer, apparently a standard Cipher scientist.
"Ah, there you are. Well done, Lipen. You may leave now." he said. Lipen didn't say a word, but left the room. This man appeared to have a lot of authority in Cipher. He started talking. "Hello, ms. Alya. You probably don't know me, so I'll introduce myself first. My name is Onjah, and I work here." "What is it you need me for?" Alya asked. "I was getting to that. To cut right to the case, I want you to work with us." Alya wasn't surprised. This had happened to many leading researchers and scientists during earlier Cipher plans. Like all the others, she would refuse, she thought. Onjah kept talking. "Knowing you, simply asking won't do us any good. So, let me just tell you that you will be working here with us from now on." This was a new one. It didn't matter. She wouldn't cooperate anyway. They couldn't force her. She knew that. Except she was wrong.
Onjah kept talking. "I suppose I'd better tell you about our plan. You see, we've improved the Shadow Change routine." "So, now you can make another Shadow pokémon per hour?" she asked sarcastically. He looked at her, then smiled. "I don't have a very good sense of humor, Alya, so I'd just keep those jokes to myself if I were you. Well, making more is only part of it. We can now make them better. They've gained a lot of new abilities I think will come in handy. First of all, they can now turn another pokémon into a Shadow pokémon without the aid of a machine. Let's just take a break there." This was bad news for the world. If she couldn't tell her father or Lorno... but she had to hear the rest too. "Go on." she said. Onjah smiled. "Nice girl. Well, unfortunately, this process takes time and concentration. It can't be done during a battle. Which is a shame. Anyway, in addition to this, the strength of a Shadow pokémon is increased many times. The pokémon you fought are good examples of this. This also makes them almost impossible to snag by normal means. I'll stop for a moment... you can let this sink in now."
Alya had seen Kyogre and Groudon. She knew how strong Shadow pokémon were. If they couldn't snag these pokémon from Cipher, they might not have even a slight chance. She sorted this out in her mind, and asked him to keep talking.
"Right. Sadly, there are a few downsides to these new Shadow pokémon. These Shadow pokémon don't get the old Shadow attacks the old ones got. They only get their original attacks. And to add to that, once they start using a move, they can't use another until they've been withdrawn. This is obviously bad. And, since you're an expert on pokémon moves, this is your job to fix. Your first task will be to allow them access to all moves at all times, and when you're done with that you'll find a way to give them Shadow attacks. Is that clear?" She attempted to sort the vulnerabilities of Shadow pokémon out in her mind. He seemed to understand that, and gave her a few minutes. After thinking it over carefully, he repeated his enquiry. "No.", she simply replied. "I suspected as much. Well, you see, I know something you don't. The Shadow pokémon have another advantage I didn't tell you about yet." This was obviously the biggest, worst part.
"They have a limited ability to add a little Shadow to people." he said. She had been right. This was the worst part. He didn't stop talking this time. "It is rather limited, though. Unlike Shadow pokémon, the darkness will eventually wear off, unless we renew it. And as you obviously know, 'closing the door to its heart' is just an expression. It's all in the brain. And like Shadow pokémon, Shadow humans can't learn anything new while it's closed. That's why I told you the plan - Because the job you're going to do requires knowledge about it. Lipen, get it done." Lipen took out a pokéball and released the pokémon inside. A Marill came out. It had to be a Shadow Marill. "Oh, one more thing." Onjah had more to add. "Remember the Kyogre, Groudon and Rayquaza that defeated your entire team? They are the prime subjects of Cipher, the strongest Shadow pokémon we have. Please don't use them as test subjects." Onjah turned his back to her, and kept working. Lipen ordered Marill to "do it". She knew what he meant. There was no sign of any emotion in his voice. She looked at Marill. It was approaching slowly. That was the last thing she knew.