Humanity's Worst Fear

A/N: Thanks to those who kindly reviewed and wanted me to continue the story! Also, I'm changing a minor detail in the prologue (thanks to Agementus for pointing that out!). Oh, and sorry for the long wait. I was busy with school work and stuff…  Anyways, here's the first chapter!

John or SPARTAN -117 was walking down the narrow hallways of the Cairo after two intense hours of workout at the special SPARTAN training gym. He was sweating hard and was ready for a nice cold shower when the overhead speakers came to life.

"SPARTAN -117 please report to the bridge immediately."

"What now", he thought, "just after 2 hours at the gym".

John slowly walked to the bridge wandering what was going on. There hasn't been much action lately, as the Covenant had been defeated and the alliance with URF. He soon arrived at the bridge where marines with heavy weaponry ranging from Jackhammers to snipers. They stepped aside as the 7 foot tall SPARTAN went through the open blast door. Admiral Hood was staring at the tactical displays when John had arrived. He quickly snapped into a salute at his commanding officer, who in turn saluted back.

"Master Chief, we are facing a major dilemma right now", Hood said with concern showing in his face.

"What is it sir?" MC asked, wandering.

"Cortana, I think it will be best if you explain", said Hood turning to the projected image of a 5 year old "Smart" AI who went with MC on numerous missions.

"Of course", Cortana turned towards to the armor-less SPARTAN. "There have been numerous whispers on our long-range probes. It shows that there are Covenant frigates and Human ships alike and all of them are heavily damaged. It's a wander that they can still move. We tried hailing them on our long-range probes, but they wouldn't respond.

Master Chief looked concerned.

"That could only mean two things," Cortana resumed, "It's either a fleet which came from who-knows-where, or-"

"The Flood", MC finished, quickly catching on.

Cortana nodded grimly.

"But how could they have found Earth?" MC wandered out loud.

"We're not exactly sure they know we're here, but there's a 79.2 chance that they do." Cortana responded.

MC sighed in frustration. "If they know we're here, Humanity is in grave danger" MC realized.

"I suggest we initiate evacuation procedures right now", Cortana advised to Admiral Hood.

"I was just about to do that," Hood said. "Cortana, send ONI the information that the Flood has found us, that we suggest evacuation right now, and send them any information we know about the Flood. I'm sure they'll want it."

"Done" Cortana said after a second or so.

"Oh, and tell the Arbiter the same thing. I think they'll want to know what's going on." Hood added.

Cortana nodded, and then disappeared.

Hood turned toward John. "Master Chief, the lives of Humanity lies on your capable hands. I herby grant you permission to take over every Marine on this station.

MC was bewildered. "But sir-"

"No buts, Master Chief. I'm giving you an order solider!" Hood stated sharply.

"Yes, sir!" MC replied. John went off to get suit up for battle.

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Meanwhile…

The Arbiter was in his quarters when the Human's AI radioed him over the intercom. "Arbiter, there's a huge problem. I suggest you get geared up."

The Arbiter nodded. He had come to trust the AI, which saved him in countless times. "What is it, Cortana?" (The Arbiter got around to using her name)

"The Flood", Cortana simply stated.

The Arbiter stopped dead in his tracks. "WHAT!"

"Just report to the bridge. Everything will be explained". Cortana responded.

The Arbiter ran to the bridge of the Cairo and met the Admiral.

"I'm sure Cortana told you that it has something to do with the Flood?" The Admiral questioned.

The Arbiter nodded.

"Well, I think they've found Earth." Hood said, concerned.

"Then I shall contact my worriers and prepare for battle."

Hood nodded in agreement. The Arbiter contacted all of URF members and told them what was going on. He ordered them to meet on the Human's home planet and get geared up. Suddenly, alarms began to ring.

"All personal, please report to both Armories." The voice talking over the speakers was definitely Hood. "You will be briefed on what is happening."

The Arbiter sped towards the nearest Armory to get weapons. To his considerable surprise, nearly everyone was there before him, even though he ran his fastest.

"Alright people," Sergeant Johnson was there, speaking over the chatters. "Here's what's going on. The Flood has found Earth-" He was cut down by surprised Marines. "-and we will destroy them one by one," Johnson continued, talking over the Marines. "Get yourself armed with bullets, but no sniper rifle. It's useless against them. No plasma weapons (since the alliance, the armories have been filled with weapons from both sides) and only frag grenades."

The Marines hustled to get themselves armed and ready for combat.

"Most of you will go down to Earth to help defend the planet, since the Flood aren't smart enough to board the stations. Once down there, your commanders will be either one of the SPARTANS-" There was excitement among the Marines for the thought of fighting alongside a SPARTAN. "-or a Sergeant, like me. Are we clear about this?" Johnson yelled.

"Sir, yes sir!" The Marines replied.

Johnson nodded with approval. "Get to the hanger bays, double time!"

In a matter of seconds, the Marines emptied the Amory and headed towards the hanger bays while Johnson headed to the bridge.

Once he arrived, John was already there with Hood and the Arbiter planning how to stop the Flood attack.

"Oh, Sergeant, you're here." Admiral Hood noticed. "Good, now we can proceed with the mission. Sergeant, we've decided to destroy all of the remaining Halos, since the Flood originates from there. Master Chief will take an Omega-classed ship with a few NOVA bombs to do that."

An Omega classed ship was rare, and new among UNSC, It was the biggest, fastest and the strongest ship ever, armed with weapons from both UNSC and Covenant alike. It has 10 Super Mac guns and countless number of other weapons. There were only a few of them ever built.

"But sir, don't we need those ships for defending Earth?" Johnson questioned.

"That's why we're only taking one," Admiral responded. "Anyways, since we have the Ark at our disposal, I'll upload the locations of the remaining Halos into Cortana. The journey starts tomorrow at 0600 hours, so get some rest. That's an order. Oh, and by the way, do not tell anyone else about the mission. Consider it Black Ops."

"Sir, yes sir! They said.

Master Chief and Sergeant Johnson went back to their respective quarters. But along the way, MC met a few of his fellow SPARTAN members.

"Hey, MC, do you want to go with us to the shooting range?" Will asked.

"No, sorry. I have to get some rest, Captain's orders." MC said.

"What did you do this time to get rest?"

"It's what I'm going to do. Black Ops mission."

"Oh." They were slightly disappointed, but continued along their way.

John slept for the rest of the day and woke up at 0500 hours to do some exercises and get geared up.