As soon as the Space Pirates took over the former Galactic Headquarters building in Veilstone City, the government began making plans to infiltrate it. They had no hope of taking it back as long as Mewtwo was there, but gathering the Pirate intelligence hidden within could be very useful to them. The Governor requested Samus's help in the mission. Samus was going to volunteer even if she hadn't been asked.
The tricky part was the timing. If they waited too long, the Pirates would have more time to build up their security. On the other hand, they couldn't rush into this – they had to gather all the intelligence they could get, and then analyze said intelligence, to be fully prepared for this task. In the end, late on the very night after the takeover, they decided that they were as prepared as they were going to be, and that the optimal time had come. It was time to break into the Pirate base.
The former Galactic Headquarters – the new Space Pirate base – was far bigger than all of the other buildings in Veilstone. The roof of the building was a huge white dome surrounded by several tall, bluish towers, which were lined with windows like an office building. Each of these towers were now equipped with searchlights; bright beams pierced the otherwise dark night, slowly moving and surveying the surrounding area. Space Pirates patrolled the streets of Veilstone, making sure nobody in the city could pose a threat to their base.
Samus watched all of this from atop a hill just outside of the city. It was very, very late; the descending crescent moon was already touching the horizon, although it took up so much of the sky that there would be another couple of hours before it fully set. But Samus wasn't looking at the moon. She had her eyes set on the large building in the distance, the one surrounded by bright lights – the one that she was about to break into. Her attention shifted, however, when visitors arrived.
One by one, nine tiny, round, brown little creatures popped out of the ground in front of Samus. These were actually three Pokémon – a trio of Dugtrio, each of which consists of three Diglet. Samus kneeled down, although this did not put her at anything close to eye-level with the tiny critters. "You're done?" she asked them. The Dugtrio bobbed up and down in apparent agreement. Then they moved to each side, allowing Samus to access the tunnel they had just finished digging. "Thanks, guys," said Samus. She entered morph ball mode, rolled over to the hole in the ground, and dropped into it.
Samus had a long way to roll – she basically rolled under the entire length of Veilstone City. The tunnel was just barely wide enough for her morph ball to fit through. However, beneath the Pirate base, the Dugtrio had dug out a large hole, around which Samus could roll freely. When Samus got to this hole at the end of the long dirt tunnel, she knew that only a thin layer of dirt and tile separated her from the base. This was the trickiest part of the entire operation – getting into the building while remaining unnoticed. Unless Samus remained unnoticed throughout this whole mission, she would once again find herself face-to-face with Mewtwo. Even with her new Phazon powers and new upgrades, there was no guarantee that she could survive a fight against him, and it was best not to find out unless it was absolutely necessary.
The Governor's science team had given Samus several items. One was a full electronic map of the building above her; the map also showed her where she was relative to the building. Using this map as her guide, Samus rolled over to the planned spot. There, she laid a bomb. The small blast cleared out the dirt around her; there was no dirt above her now, only concrete. To enter the building, Samus would have to blast through that concrete. But not yet – the Pirates would notice. It was time to create a distraction.
Samus rolled over to a spot on the opposite side of the building, near the edge. Above her, the Dugtrio had pushed a dead Electrode aboveground. It was still halfway buried, and positioned just out of reach of the spotlights, but if the Pirates searched the grounds around the building, they would easily find it. It would therefore be blamed for the following explosion. Specifically, the explosion resulting from the Power Bomb that Samus then used. It was very noisy, and would shake the ground above her and possibly crack the floor of the base. All Space Pirates on the first level would go rushing to that spot to investigate the commotion. In theory.
Samus quickly rolled back to the spot she had bombed earlier and planted another bomb. This one crumbled the concrete above. Samus now assumed her normal form. She reached through the concrete debris to find the bottom of the tile floor. Swiftly yet cautiously, she lifted one of the tiles and peeked into the building.
The distraction had worked – there were no Space Pirates in sight. They were all behind several walls, where Samus had created a scene by laying a Power Bomb. The specific tile she was under had not been chosen at random – this was one of the only spots on this floor that was not monitored by a camera. A camera on the wall above Samus monitored everything else in the room. Samus shot a Wave Beam at the camera to short-circuit it. With any luck, this would be the only time she'd have to do that; if she short-circuited too many cameras, it wouldn't be long before the Pirates noticed.
Samus put the tile aside and lifted herself onto the floor. Then she put the tile back in place, making sure to leave no hint that anyone had done anything to it. On a nearby wall was an air vent. Samus now made all of her armor disappear, leaving only her skin-tight Zero Suit on. Samus carefully removed the cover to the air vent and crawled inside. She got in feet-first so that she could put the cover back on behind her.
Samus crawled backwards through the ventilation duct, trying to make as little noise as possible. She had to lie on her belly the whole time in order to fit; the ducts were not very wide. Finally, she got to a corner where the duct went upward. Here, she curled up, putting her chin between her knees, and then activated her armor. It was not easy to go from being armorless to a morph ball in one step, but it could be done. In this case, it was necessary – there was not enough room for her fully-armored figure to fit. There was, however, plenty of room for her morph ball form.
Samus had yet to find her Spider Ball upgrade on this planet, assuming that it existed. In its place, the Governor's science team had fitted a series of electromagnets onto her armor. It wasn't as smooth as her normal Spider Ball, and it was a temporary solution – the tiniest damage would eliminate these things. Still, as a makeshift replacement, it worked like a charm. Samus magnetically attached herself to the metallic duct and rolled upwards. Not only did this "Spider Ball" allow Samus to scale the vertical ducts, it allowed her to do so almost noiselessly.
Up she rolled, until, finally, she got to a fork. Above her was a fan; she could either go along the wall of the building or roll inside of the second floor ceiling. Samus chose the latter. Onwards through the duct she rolled. Occasionally, she passed by a vent through which she could see beneath her. For a while, she saw nothing but empty hallways through these vents. But eventually, she got to a dead end, and the vent beneath her revealed quite an interesting room.
Huge monitors lined the walls. These were displaying diagrams for some sort of machine, as well as the innards of… something biological. Samus couldn't quite tell what. Nonetheless, she scanned these monitors and transmitted the data to the Capitol. The room was filled with computers, although at the moment, only one Space Pirate was sitting at one of them. Presumably, the rest were off sleeping somewhere. Samus scanned the computers and hacked through the coded information. Most of it was maintenance data – information about the two Pirate bases (this one and Mt. Chimney) and their upkeep. Samus only skimmed most of this data as she transmitted it. Eventually, she found an interesting gem of information within one of the computers. Samus read the piece of Space Pirate data:
MT. CORONET
The machine codenamed "Apokélypse" is complete and fully operational. As planned, the machine is integrated with Mt. Coronet. At this stage in the plan, no location is more vital to our success than this mountain. Our Metroids, having completed most of their duties, are now safely stored within the mountain. Atop the mountain, at the location known as "Spear Pillar", rests Mother Brain. Her reconstruction is complete. However, this Mother Brain is not the super-intelligent being who led us on Zebes. She is little more than a dumb machine, or a biological computer. Nor does she have her body, as we did not have time to rebuild it. She serves as the head of the machine. She also maintains control of the Metroids. Her survival is our number one priority. Spear Pillar must be guarded at all costs.
Each new fact in this piece of data shocked Samus more than the last. Apokélypse? Metroids in Mt. Coronet? But worst of all… Mother Brain was back. Samus couldn't be more filled with dread. She had desperately hoped that she'd seen the last of her old nemesis. Apparently not. And it seemed that defeating this new Mother Brain was crucial to stopping the Space Pirates. That was the spark of light within the dread: they now had a lead. Thanks to this piece of data, they now knew what to do to stop the Pirates as well as where. The only questions remaining were how and why.
Samus was finished scanning the computers. Being at a dead end, she turned back and backtracked through the duct. When she got back to the fork, she turned left to move parallel to the building's outer wall. She kept rolling until the duct turned upward. Once again, she ascended the duct, passing by a couple more forks as she rose. This ventilation system was like a maze, Samus marveled. Soon she found the fork at which she could roll through the ducts above the third story ceiling. She made a turn in order to do so.
In the third floor, Samus passed by a couple of rooms where several unarmored Space Pirates slept. When she found herself above another computer lab, she was disappointed to find that most of the computers were off, and so she couldn't hack into them. But one of them was still on. And this one held what might be a highly valuable piece of data:
OPERATION GIGADRAIN
The project codenamed "Operation Gigadrain" has been mostly successful. As planned, our Metroids drained the Life Energy of the three legendary beasts of Johto, Kyogre, the Regi trio, Regigigas, and the three lake guardians of Sinnoh. They acted under the control of our leader, but the addition of Mother Brain strengthened this control. Under this stronger control, the Metroids were made to transfer the Life Energy into the nodes within Mt. Coronet, giving it to the machine codenamed "Apokélypse". Life Energy from the meteorites we harvested has been transferred to the machine as well. Unfortunately, a setback may have put the plan on hold. Because of our defeat at the Weather Institute, we were not able to find Groudon or Rayquaza. Without their Life Energy, it is unlikely that the final step in our plan can be executed properly. It is not clear how we will compensate for this loss, but surely it can be done.
Well, that explained why the Pirates were after Life Energy. Except not really. They wanted it for their machine, but what did this machine do? Questions were still plentiful. Unsatisfied, Samus continued rolling forwards.
The duct went all the way to the wall on the other side of the building. There, Samus turned upwards to ascend the building further. But now the path became less straightforward. Samus, wanting to investigate the fourth floor, rolled down a path towards the building's interior. But there she found herself going through a maze-like labyrinth of twists and turns, all without any vents to see the main floor through. Finally, she made it to a vent on the wall; she peered through the vent and saw that it was in the middle of a wide hallway. What she saw in the hallway made her roll backwards a little to make sure she remained unseen.
"…Just an Electrode," a large Space Pirate was saying to its leader, Mewtwo. "We do not know how it got there, but Electrode are not native to this area."
"Possibly it was a test by our enemies," said Mewtwo. "Perhaps they wanted to see exactly what they could get away with under our noses. The fact that the Electrode got so close to the building without detection is troubling. Have you checked the security cameras yet?"
Even in her morph ball form, Samus could feel herself tense up. "Yes," answered the Pirate. "No suspicious activity was recorded. But…."
"But?"
"But… for an unknown reason, one of the cameras on the first floor went black. But it is not close to any possible entry points, and since it was the only camera to do so, it was probably just a flaw in the design."
"Faulty cameras are the last thing I want to deal with right now." Mewtwo looked at the Pirate with disgust, as if this were its fault. "Security in this place needs to be tightened as soon as possible. For one thing, I want motion sensors installed in the air ducts." Mewtwo may have been a monster, but Samus had to admit that he was a clever one. No wonder the Governor considered himself to be in a proxy battle of wits with him.
"But sir… there's no way to access the air ducts from the outside," said the Pirate. It spoke with a tremble in its voice, probably knowing that it would be scolded for speaking up.
"Don't tell me what I already know, idiot," said Mewtwo. "Yes, it is impossible to sneak in using the air ducts, but that is not the issue. Should someone manage to break into the building, they could use the ducts to sneak around without getting caught. The Hunter in particular could easily do this using her morph ball ability. We must not underestimate our enemies. They are more cunning than they may at first seem. But then, I wouldn't have it any other way." Mewtwo turned away from the Pirate and started walking down the hall. The Pirate followed. "As I said, I want sensors in the air ducts, and I want it done soon. I'm entrusting you with this information, for in a moment I will be gone. I know that it will be done by the time I get back. Or else."
"Get back from what, sir?"
"From the Leviathan Seed." Samus knew what this was – Leviathan Seeds were the huge meteors that corrupted planets with Phazon. They would launch from their home world of Phaaze and then generate wormholes to travel through space and find a planet to spread Phazon to. But Samus had destroyed the planet Phaaze and, supposedly, eliminated all Phazon and Leviathan Seeds as well. Supposedly. If one Leviathan had somehow survived, Samus neither knew how nor where it was.
Mewtwo stopped walking when he reached a large metallic door. "The blunder at the Weather Institute has cost us dearly," he continued. "Even with everything in place, we cannot begin the final phase with the inadequate amount of Life Energy in our possession. At the Leviathan, I will have to replenish my bodily supply of Phazon to make up the difference. Thus, I, personally, will wield enough power to see the machine function successfully. Tell your comrades this: while I am gone, you are not – I repeat, NOT – to make any unplanned moves. Until I return, the rest of you are to sit still and not draw attention to yourselves. If there's one thing the massive failure at Goldenrod City taught me, it's that I can't trust you idiots to do anything on your own. In fact, because of that failure, you never obtained the TurboTransceiver from the Radio Tower and will thus be unable to communicate with me when I'm gone."
Next to the door was an electronic panel with numbered buttons. Mewtwo entered an eight-digit code in this panel; Samus made sure to memorize it. The door opened. The room behind it was mostly empty. Two Space Pirates stood as if in guard of something. A pedestal stood between them, and on top of this pedestal was a Pokéball.
"Here are your instructions," Mewtwo said to the large Pirate. "I am to be released from my Pokéball tomorrow at sundown. Release me earlier if and ONLY if it is absolutely necessary. Otherwise, you are to do what is necessary to keep our bases of operation safe and nothing more. Understand?"
"Yes, sir!" said the Pirate.
Mewtwo walked past the threshold of the open door, but then stopped. "You do know who the previous owner of this building was, don't you?" he asked out of nowhere.
"Y…Yes, Master," said the Pirate in the hall. "I believe it was a group known as Team Galactic, led by a man named Cyrus."
"That is correct," said Mewtwo. "It is because of this man's effort that we were able to duplicate the Red Chain using the technology we found in this very building. And it is in part because of this that we were able to detain Dialga, Palkia, and Girantina, and to integrate them with the Apokélypse machine. Now, tell me: do you know what this man Cyrus attempted to do?"
"I've… heard a little. Did he not try to recreate the universe using the power of Dialga and Palkia?"
"That is correct. But he failed, and miserably at that. Do you know why?"
"No, sir… why?"
Mewtwo sighed. "Of course you wouldn't know. Very well, I will explain. Cyrus failed because he did not grasp the bigger picture. He saw two godlike Pokémon and wanted their powers to himself, not realizing that these Pokémon are little more than the limbs of a larger cosmic body. If you grab a man's right arm, he will punch you with his left arm. If you grab both arms, he will kick you instead. This is how Cyrus failed – he tried to control one limb, and the others revolted. We will not make the same mistake. Our aim is nothing less than control of the head. We will take control of Oscelon, and the universe shall become our playground. Soon, all that is will be like an eternal fight, or like a game that never ends. Because we see the bigger picture. That is why we will win." And then the metal door slid shut behind him.
The large Pirate in the hall quickly walked out of sight. Then, from behind the metal door, Samus faintly heard what sounded to her like a Pokéball opening.
Samus now faced a dilemma. Mewtwo had strongly implied that he was entering his Pokéball. Now she heard what she could swear was a Pokéball opening in the room he just entered. Was Mewtwo really inside his Pokéball right now? If so, this was the most perfect opportunity Samus was ever going to get. But if she was wrong… Mewtwo could be standing right behind that door, waiting for her. Was this a trap? Had Mewtwo known that she was listening in on him, and was trying to lure her out? But if so, why hadn't he attacked her already? Samus knew she couldn't use the ducts to inspect this room –she'd seen no vents when she looked inside. There was only one way in and out, and that was the door unlocked by the eight-digit code. In the end, Samus decided that this was an opportunity she could not afford to pass up. It was a risk she had to take.
She waited a minute to make sure that the coast was clear. Then she bombed open the cover to the vent in front of her. She rolled out of the vent and transformed from a morph ball into her normal figure. Cautiously, she walked over to the room Mewtwo had gone into. On the panel next to it, she inputted the numerical code she had memorized. The door slid open to reveal what awaited her.
What awaited her was two Space Pirates, a pedestal between them, and a Pokéball on top of that pedestal. That was it. No Mewtwo. Samus was relieved, but not so relieved as to forget to take care of the two Pirate guards. She barraged them with missiles right away; after a delayed response, they fired back at her, but Samus dodged their fire. Soon, they were both dead on the floor. Samus walked over to the pedestal. She placed her hand over the Pokéball. Then all of the lights turned red and an extremely loud alarm sounded.
Ignoring the commotion, Samus converted the Pokéball into energy and absorbed it into her suit's storage system. Once that was done, she could no longer ignore the commotion. First of all, she opened a flap on her Arm Cannon to press a series of buttons that would call her ship over. Over the loud alarm, she could hear what sounded like a stampede of Space Pirates rushing down the hall in her direction. Samus ran out of the room to find that this was exactly what it sounded like. The group of Pirates began shooting at her; Samus ran towards them and shot back. Then she surprised them by jumping into the air and using her Screw Attack. She sliced through the group of Pirates like a knife through butter, emerging behind them. The Pirates turned around and chased Samus in the other direction, but she was much faster than they were. She quickly turned a corner and then, barely two seconds later, turned another corner, putting her out of their view. But unless she kept running, they were bound to catch up with her eventually.
Samus suddenly found her path blocked by two very large, Phazon-enhanced Space Pirates. It was time to enter Hyper Mode. In Hyper Mode, Samus sacrificed a little of her own energy to temporarily induce a state in which she could use Phazon as a weapon. Samus and the two Pirates fought briefly, but the group behind them was catching up. Samus became a morph ball, rolled forward, and planted a Power Bomb. The forceful explosion that followed knocked both Pirates onto the ground. Samus exited her morph ball form and kept running; she did not need to defeat these Space Pirates now, only to escape.
She turned another corner; there, a lone Pirate Trooper awaited her. She slammed into it with her Screw Attack, then shot it with her Ice Beam repeatedly while it was down. It became totally immobilized, and Samus kept running. One hallway later, she found what she was looking for: the windows. The huge glass windows covered the entire wall; through it, she could see the lights of Veilstone City. Behind her, she could just barely hear the sound of approaching Space Pirates over the alarm. Samus jumped, used Screw Attack, and crashed through the window.
Samus's timing was perfect: she fell about two stories down until her gunship caught her. She quickly entered the gunship via the emergency hatch at its top. Space Pirates fired at the ship both from the roof and through the shattered window, but the ship dodged all oncoming attacks.
Before leaving, Samus decided to give the Pirates one last bit of trouble. She steered the gunship away from the Pirate base, making it seem as though she were leaving. Then the ship turned around and sped towards the base again. Space Pirates continued to fire at it, and continued to miss. When the gunship was right above the base, Samus dropped a ship missile. It hit the Pirate base and blew its roof to smithereens. Satisfied, Samus flew her ship away.
The operation was more successful than Samus could ever have hoped. She had the information she had sought. She'd greatly damaged the top of the Pirate base. And, most importantly, she was now in possession of Mewtwo's Pokéball… with Mewtwo inside it.
As planned, Samus met back with the Governor at Professor Rowan's lab in Sandgem Town. There, Samus told her tale of triumph to Rowan and the Governor. The three of them then had to decide what to do with Mewtwo's Pokéball. They could keep it safe, but the Space Pirates would almost certainly try to get it back, and even a small chance of them succeeding was too much to risk. They also discussed the possibility of creating an unfavorable environment to release Mewtwo into in order to trap him and/or defeat him. But this was the riskiest option of all; a long list of things could go wrong, and then they'd find themselves in a worse position than ever. In the end, it was decided that the Pokéball had to be destroyed. Perhaps this would eliminate any usefulness it might have served them, but it was the best option available.
Early the next morning, Samus got a distress signal from Jude Tutino. He told her what she already knew: that Mt. Coronet was infested with Metroids.
"Stay where you are for now," Samus told him. "I'll contact you again soon. We're coming up with a plan."