Author's Notes: This is my first fanfic, I've decided to do a Halo, Metroid crossover. I don't plan on having every chapter telling all 4 points of view each time, I just thought it would be a good idea to do it the first chapter, to give a clear idea of where the characters are starting out from. This takes place right after Halo 2, and 3 months after Metroid: Fusion. Hope you enjoy it, I've done my best to not bastardize either franchises.

Halo-Metroid: Crisis Rising

Chapter One

High Charity Ruins
10.21.2552(Military Calendar)
22:25

"I will ask, and you will answer." said the Gravemind as it stretched it's tentacles towards the Holopanel. Cortana raised a hand to stop them. If she was separated from the city network, she would be useless, not only to the Master Chief, but to this thing too. Obviously it had come in the In Amber Clad, bringing the Flood with it. The tentacles may be right in front of her, but she knew that the actual Gravemind was residing (possibly unable to get out of) that ship. She needed time; she would have to go along with the Gravemind for now.

"All right, shoot."

"Where has the ship of the ancient ones, 'fore runners', gone to?"

Cortana pondered how she would answer the question. Telling this thing about Earth would be a bad idea. Then again, lying to this creature would be a bad idea as well. But, the Gravemind had no possible way to get to Earth. Even if the In Amber Clad could still run, she could detonate it before it got a chance to activate its slip-space drive. Any remaining covenant ship that hadn't been used for evacuation was too small to enter slip-space without destroying the shuttle.

"It's heading to the planet Earth. If you're thinking about stopping them, which you more than likely are, forget it. There's no ship here that can take you to a location so far away."

"That does not concern me. I have sent the Reclaimer you call 'spartan', to take care of the matter concerning the Ark. I am not in a hurry, though I assure I will make my way there in time. I have listened to what your enemies know of the human race, I am not ignorant of what obstacles await them at the Ark."

Cortana logged into the network's surveillance systems to overlook the city. There was not a trace of food for the Flood; the last group of covenant on the city, several elites and hunters, escaped on a phantom about ten minutes ago. Now that there was no way to quench their insatiable hunger, the Flood were tame. Clearly the Gravemind was their leader; they all stationed themselves at the wrecked ship containing it. The only exception was a large group waiting expectantly at the largest dock in High Charity. They all had their heads turned towards the sky. Cortana moved the camera view up to try to see what they were looking at, nothing. This was very odd, and more than a little unsettling.

"Now I want to ask you a question. What exactly are you, Gravemind?"

She quickly went back to surveillance to see if the Flood at the landing dock had changed at all.

"I am a creation of the ancient race you call Fore-runners. When they discovered the Flood, they wanted to use them as Bio-Weapons against an enemy race of theirs. The conflict that led them to this is irrelevant. Both races are extinct and long-gone; their outstanding technologies now remain as their only testament. When they tried to bring sentience and obedience to the Flood, I was the only successful product of their experimentation.

But, when other less successful experiments went beyond their control, there was an outbreak. They were forced to activate the rings, and I was contained safe inside one of those rings. I am the only intelligent form of Flood. I have control over my kind; I alone can bring order and tactical formation for battle like the Fore-runners had always planned."

"Like the way you have all of them situated by your taxi ship?" Cortana asked.

"Well, not all of them…" The Gravemind replied, with a sinister chuckle.

Cortana, not liking that response, immediately switched back to surveillance. The Flood by the dock were running haphazardly around the dock with excitement as they gazed upward. Cortana moved the camera view upward again to see a ship starting to descend. The Flood stopped their wayward movement and, as if directed to, they took positions in hiding places that the ship would never see them in.

Now the Flood station by the In Amber Clad began marching in ranks like troops, in the direction of the landing dock. Cortana gasped, a habit she had picked up from humans, at the sight. She quickly activated the emergency alarm for the docking area, but the ship didn't take any heed at all to the alarms.

"Heh, heh, heh… I did tell you that I will make my way there in time, did I not?"

Location Unknown-Far beyond Galactic Federation Borders
2-19 20X9(Cosmic Year)
18.87 Hours

It had been nearly three months since her mission in the Biological Space Labs against the X parasites. The Galactic Federation had not taken her direct violation of their orders well. They had asked her to abort her mission when they got the idea that the X parasites which had overrun the space station could be used as a biological weapon. Knowing that the risk of another outbreak was too great, Samus had set the station on a collision course with the adjacent planet that the X parasites had come from. This made a successful destruction of the entire X parasite species, doing the Federation a favor they would never appreciate. They wanted her to come in for personal questioning, but Samus wouldn't allow it. She knew that "personal questioning", meant interrogation in a building where they could throw her in a cell for however long they damn well pleased. She would only answer the questions of the rabid politicians and leaders via telecommunication.

She didn't have the time to go to the Galactic Federation headquarters anyway. Not even a full hour after destroying the station and that hellhole planet, she had been attacked by rogue Space Pirate battleships. They had left in a hurry when she returned fire, and she had been following them ever since.

Now she was in a part of the universe completely uncharted and unknown. The blue green planet she was staring at right now was the first thing she had seen in about five days.

At that moment the A.I on her ship, named Adam, interrupted her thoughts.

"Samus, there are two artificial structures up ahead, orbiting this planet. There is also a Space Pirate ship docking on one of the structures."

Samus leaned forward and tried to see what Adam was talking about. She couldn't see the two things Adam had mentioned, but didn't care.

"Then speed up the ship and take us right to that Space Pirate ship. We're in pursuit of them, and don't have a second to spare."

As the ship accelerated, she could finally see the two objects in orbit around the planet. One was a large ring, and the other looked like a city station. Oddly enough, the city station seemed to be devoid of light, or any semblance of electricity. When she asked Adam about it, he said the same thing.

"Their power source has been disengaged for a short while; some of the systems seem to be working on residual power. The city is called 'High Charity', and it's broadcasting an emergency warning signal. The Space Pirates have taken no notice of it."

"Then neither will we Adam, take us down. Drop me off at the other end of the city, away from the Space Pirates. Then I want you to go somewhere hidden and safe, preferably off the ground and safe from whatever might have warranted that emergency signal."

As the ship swooped down upon the city, Samus could see nothing but seemingly empty buildings. The largest of them stood in the center of the city imposingly. Adam came to a halt right in front of it. Samus leaped out of the above hatch and did a graceful flip onto the ground.

"The broadcast is coming from a location right only a few kilometers next to a crash site. If you go in the direction of the smoke on the other side of this building, you'll reach it. That seems to be where the Space Pirates are landing, I didn't have enough time to scan the area. I could detect an extremely high level of activity there though, be careful."

"Thank you Adam, I'll get in touch with you when something happens."

Samus turned to the doors of looming building, and walked in. It was absolute darkness in there, so she put on her heat visor. There was nothing as far as she could see, the hallway she had stepped into was empty. There was nothing but discarded weapons and doors that looked like they had been forced open. As Samus proceeded through the halls, she still saw nothing. After the first five minutes, she decided to pick up the pace and start running. The clanking sound of her metallic foot steps echoed off the walls, and she tried every other visor she had to try to find anything out of the ordinary. Still nothing.

Then she stepped into a large chamber, there was remnants of a large scale fight her, there were more dropped weapons and shards of armor here than any other room she had been in so far. Over at a corner were some bodies, the first she had seen. The bodies were heavily armored, and on their right arms were permanently wielded cannons. Only a little bit of the flesh underneath the armor could be seen in the neck, and lower torso regions. She kicked one of the bodies over, and saw several little monsters that looked like squid feeding on its flesh.

They turned to look at her, and Samus scanned them quickly. They were parasitic, reproduced very quickly, and had an extremely low body temperature. That was all the information her scan visor could tell her. She fired her cannon at them, destroying all three of them with two shots. It was the only interesting thing that would happen to her until she finally got to the other end of the building.

About ten minutes later, Samus blew a hole through the last door she would have to walk through. When she stepped through, she finally saw what had caused the disaster on High Charity. All around her, parasite and Space Pirate were engaged in frenetic combat.

Halo activation structure
Ninth Age of reclamation
22:35(human time)

Sergeant Johnson looked to the Arbiter and asked, "So how do we get off this ring, and back to earth?"

"There are plenty of Phantoms in the area, especially now that the Brutes here have been eliminated. Unfortunately those can't take us all the way to Earth. Unless we find a ship large enough to have a slip-space drive here, the fastest way would be to take a phantom to High Charity and steal ourselves a ship from there. Either way, I don't want to leave the ring without taking some of my allies with us."

Captain Keyes was not in their conversation at all. Instead, she was throwing questions at 343 Guilty Spark concerning Earth, the Ark, and the other Halos.

"I am afraid that the Ark needs no index in order to be activated, young Reclaimer. Once the Ark is activated, every Halo in the universe will trigger, leaving all life in the universe dead; with the exception of those on the Ark, of course."

"Well, we better figure out what we're going to do and make it snappy. I think you better find your friends quickly if we're going to get to Earth in time." the sergeant remarked.

But there was no need; Elites, Hunters, and Grunts were marching in droves through the doorway. Some of them pointed their guns hesitantly at the humans, but most were just happy to see the dead bodies of the brutes. An Elite wearing white armor stepped forth from the crowd and addressed the Arbiter.

"Arbiter, we all heard what you just said while we were walking down the hall. I can tell you all ready that there isn't a ship bigger than a Phantom to spare. Several of our number have just come from High Charity. I'm afraid I have no good news to report of that once holy city. The Flood have infested the entire place, by now it'll be a wasteland. The Prophet of Truth took a ship to Earth right before the Flood outbreak started, and the remainder of the Covenant army is with him."

"Damn it! Do you have any good news for us then, big guy?" the Sergeant asked.

"No, and I actually have a little more bad news. Since the number of the Covenant Army has been halved because of the rebellion, they have contacted some allies from a remote sector of the galaxy."

"I've never heard of the Prophets allying themselves with anybody unless they became a member of the Covenant! Brother, our own leaders have committed a heresy! Who are they?"

"They are a shady orgranization called, 'Space Pirates'."

Earth's Orbit
10.21.2552(Military Calendar)
22:30

"Update me on our situation Admiral Hood."

"Well Master Chief, it's pretty bad. The Covenant army had us at stalemate until we can get more reinforcements here. Unfortunately, that takes a while, and they still haven't arrived yet. But now, the Covenant seems to have brought reinforcements of their own. I've never seen or heard of these before, but they call themselves 'Space Pirates'. They're not as advanced with their technology as the Covenant is, but they've got some pretty big numbers. We're losing Chief, and I have no idea when our reinforcements will get here, or where they are. Would care to update me on yours? How did you get here, and what is that ship?"

"This ship is a Fore-runner ship, and right now I am a stowaway on it. In here is the Prophet of Truth, along with the High Guard."

"-Ah, well that explains why your ship now has an entire Covenant fleet in defensive formation around it. We couldn't blow it out of the sky if we wanted to. What happened when Keyes followed that Covenant ship into slip-space?"

"Well sir, we found another Halo. I was able to take out the Prophet of Regret, and I also reached a Covenant city next to the Halo. Now the Covenant city is overrun by Flood, and the Prophet of Mercy is dead as well. The Covenant thinks this is holy ground, and they intend to finish what they started. I had to leave Cortana back on the city; there was a group of Brutes making their way to Halo to activate it. Considering the fact that we aren't all dead yet, either the Brutes weren't successful, or Cortana was."