Halo: Retaliation

This is the sequel to Halo: Annihilation, and as it's precursor, this is pretty off from canon.
==Summary==
3 Weeks have passed since the Human-Separatist alliance had retaken Earth. The small force had successfully defended the Human city Last Hope from the Covenant Loyalists, and have total control of the planet, the Moon, and the surrounding space. 
The Next goal for the alliance is to gather reinforcements, and ultimately head for High Charity to destroy the Covenant once and for all.
==dramatis personae==
UNSC:
*Spartans
**Spartan-007 CJ
**Spartan-051 Kurt
**Spartan-058 Linda
**Spartan-087 Kelly
**Spartan-099 Mark
**Spartan-104 Frederic
**Spartan-117 John
**Spartan-118 Allen
**Spartan-128 Donna
**About 500 Spartan-IIIs
*Marine Corps
**Lieutenant Colonel Avery "A.J." Johnson
**Corporal Hank Graves
**2nd Lieutenant Marcus Neal
**Uncounted Marines, estimated at 10,000
*Naval Personnel
**Ensign Garth Duncan
**Around 1,000 other personnel
*AI
**Cortana
**Mariah
Covenant Separatists:
*Commanders
**Grand Commander, Supreme Leader of Covenant Separatists
**Rtas 'Vadumee, Special Operations Commander
**Orkka 'Regumee, SpecOps Officer
**Ssfa 'Jcoree, Imperial Admiral
*Ground Troops
**Estimated 50,000 Elites
**Estimated 1,000,000 Grunts
**Around 500 Hunters
Covenant Loyalists:
*Commanders
**High Prophet of Mercy
*Ground Troops
**Estimated 50,000 Brutes
**Estimated 500,000 Grunts
**Estimated 100,000 Jackals
The Flood:
*The Gravemind
**At least 2,000 Combat Forms
**Unknown Infection Forms
**Unknown Carrier Forms
==Prologue==
Several Covenant frigates drifted through space, gathering every functional UNSC ship they could find. 
The Humans would be useful in ground engagements, but they hadn't the slightest idea how to control Covenant ships. Thus, the Alliance gathered every UNSC ship remotely within operational function, and repairing them.
Thus far, a good deal of ships were in working order:
*18 Frigates
*11 Destroyers
*7 Halcyon Cruisers
*5 Marathon Cruisers
*4 Wyvern Battlecruisers
*2 Carriers
*1 Repair Station
These ships were enough to match about a quarter of the Separatist fleet, but it would have to do.
...
On board the Covenant Frigate Divine Intervention's bridge, Spartan-118 Allen, and Spartan-007 CJ, were directing the ship's search for any remaining ships.
Allen scoured the radar, looking for any heat from a ship's reactor. Finally, he succeeded.
"There." He pointed on the map to a ship floating, dead in space. It was a Marathon Cruiser, one of the most powerful ships in the UNSC's fleet. 
The Frigate pulled alongside it, and several dozen boarding craft, including the Spartans, and the crew and soldiers needed to man and garrison the ship, pulled into the airlocks.
The ship was surprisingly intact. It seemed as if the Covenant had shot it once and then forgotten it. As the two Spartans, along with the bridge crew, walked towards the bridge, Allen became more and more suspicious. Finally, they reached the bridge. One of the Crewmen opened the door, and without warning, over a dozen balloon-like creatures tumbled out of the bridge.
The Spartans reacted immediately, taking out the balloons with quick bursts of their Assault Rifles. Less than 10 seconds later, they were all dead.
"Jesus!" CJ remarked. "Were those what I think they were?"
"Yes." Allen replied.
"Flood."
==Preparation==
Meanwhile, the rest of Hammer Team, and Blue Team, consisting of John a.k.a. "The Master Chief", Fred, Linda, and Kelly, were in the Captain's bunk of the UNSC Carrier Antietam. They had just gotten the message from Allen about the Flood, and had every ship, UNSC and Covenant alike, scoured for more of the disgusting creatures. They had found nothing, and were currently reporting back to Allen.
"I see." Allen said. "I'm relieved and disturbed that there weren't more of them. They always seem to travel in large numbers."
"Perhaps most of them starved?" John replied.
"Possibly. Either way, keep your eyes open. With what we'll be dealing with the next few weeks, the Flood will be the least of our worries."
I doubt that. John thought to himself.
...
The Bridge crew for the recently-commandeered Marathon Phoenix had finally settled in, and CJ had been put in charge of the ship. He approached the Captain's chair, and sat down. It barely held his weight with the Mjolnir armor, but it was comfortable anyways. He nearly jolted when light began to swirl around the holo-projector next to him. It finally settled and formed into a human figure. That of a young girl, probably only 10.
"Hello, there! I'm Mariah."
CJ was terribly confused. And angry that she had been able to scare him.
"Hello. Are you the ship's AI?"
"Yes, I am."
"I see. Could you answer a question for me? Are there any more of those Flood on the ship?"
"Flood? Scanning... Oh, I see. No, there are no more Flood on this ship. But I can't say for the others. My scanners can't detect the interiors of the other ships. You'd need a stealth ship, like a Prowler to do that."
"A Prowler, huh? Figures we're fresh out."
...
On board the Assault Carrier "Joyous Repentance", The Grand Commander, leader of the Covenant Separatists, was directing the entire Separatist fleet of nearly 150 ships at once. It was difficult, but it needed to be done if they were ever going to leave. After 3 weeks of Preparation, the final countdown had begun before all Alliance ships would jump to the nearest Covenant fleet, to spread the words of the Separatists. The Grand Commander recalled that just a day's jump from Earth would lead them to an extremely large fleet of over 300 ships. Hopefully, the Elites would join their cause. If not, they would move on.
"Sir. Exactly 2 deci-units" (20 minutes) "until the jump. The Human's will jump just before us, due to their slower jumps." Rtas 'Vadum, the Grand Commander's second-in-command, stated.
"Very well, Rtas. Send the message now."
All of the ship, Human and Covenant, lined up in formation, with just five minutes before the Human's jump.
The counter clicked down, until there were 5 seconds left.
5...4...3...2...1...
The Human fleet took off all at once, making a huge white rip in space. 10 minutes later, the Covenant followed.
The beginning of the end, had begun.
==Roundin' up the Cattle==
A day later, just as the Commander had predicted, the Alliance's fleet pulled out of Slipspace, arriving at a small desert-like planet, with only the smallest bits of Jungle.
"Whoa," CJ said. "Did the Covenant glass this place, or was it always like this?"
"Latter." Allen said. "We found a way to live on it anyway: Underground, and in the Rainforest." I don't know why there's so many Covenant stationed here, if the Commander's right, but they must be after something. We need to make sure they don't get it."
"Warning;" Mariah stated over FLEETCOM "Covenant ships inbound. Total number: 289 Frigates, 19 Destroyers, 20 CCS-class Cruisers, 5 Carriers, and 2 Assault Carriers and counting."
"What? We can't fight that many!" That was one of the Soldiers placed in command of the Halcyon Cruiser "Old Faithful".
"Relax soldier." That was Lieutenant Colonel Avery Johnson, Commander of UNSC ground forces. "Watch this."
He pressed a button, and the speech of the Grand Commander hacked onto every ship in-system.
"Sangheili! Lekgolo! Unggoy! It is I. What the Prophets stated are false! I am not dead. I could not be more alive. It is with a heavy heart I must say, our Prophets are false, my brothers! The Prophets, at this very moment, are planning our downfall with the Jiralhanae! Brothers, heed my call! Cast down our old rivals once and for all! But do not fear. You are not alone in this battle!"
At that moment, the UNSC-Covenant fleet appeared less than 10 kilometers from the edge of the fleet.
"Attack!"
At that moment, the Covenant fleet fired upon one another. A message was hastily sent to the Commander, tagging over 280 ships as "friendlies". Only a quarter of that number remained Brute-controlled. 
Rtas sent the message to every ship in the fleet, and the Alliance fleet became embroiled in the fight as well.
...
"Oh son of a --"
CJ had no time to finish his sentence, as a Loyalist frigate fired upon the Phoenix, blasting away a small chunk of the cruiser's Titanium-A armor.
"Mariah, status report!"
"Over a third of the armor in the lower decks were blown away. That was merely a scraping shot. A direct hit there will most likely gut us."
"That complicates things, doesn't it?" He turned to the man at the Navigation console.
"Ensign Garth! Turn us to face that frigate now!"
"Yes sir!"
The Phoenix lurched as it made a near 90-degree angle turn. It face the broadside of the Frigate, which had begun to warm up it's turrets for a second volley.
"Fire both MAC cannons now!" CJ yelled.
"Aye, sir!"
The ship rocked as the two MAC cannons fired in succession. The twin thunderbolts struck the Frigate, the first blasting away it's shields, the second hitting it's reactor, detonating the entire ship.
"Admiral-118, sir! Our last target has been destroyed."
"That's very nice!" Cody yelled over the COMM. "Now do you mind giving us some help?!"
Cody's Destroyer was, along with about half of the UNSC ships, embroiled in battle with a Loyalist Assault Carrier. It had destroyed 3 Frigates and a Halcyon, and looked prepared to send the rest of the fleet to the same fate.
CJ got an idea.
"Mariah, when was this planet abandoned?"
"Somewhere around 2530. Why?"
"Open a COMM channel to all known UNSC frequencies; direct it toward the planet"
"Done. Now would you mind answering what you're doing?"
CJ whistled a six-note tune into the COMM.
"What is that?"
"Oly Oly Oxen Free."
Almost immediately, over a dozen UNSC cruisers swung around the planet, striking the Assault Carrier with their guns, and taking down it's shields. Cody's ship opened fire, taking out the bridge of the ship, as several Separatist Cruisers finished it off.
...
As several ships were repaired, one of the Cruisers that had appeared from the abandoned planet docked with the Antietam. John and Allen were there to greet whoever commanded the ship.
The door opened and a man in Mjolnir armor stepped up to John. Even with his armor on, John knew this was his old friend, Kurt. Before John had time to speak, more men and women stepped onto the docking bay. They had what appeared to be Mjolnir armor, but upon closer inspection, John saw that there were many differences; one of the biggest being that the battery pack had a cloaking device attached.
"John, I'd like you to meet the SPARTAN-IIIs."
John surveyed the new "Spartans". There were over 400 and counting, more than three times the original number of Spartan IIs.
"Very nice. But what were they doing out here, so far away from Earth?"
"John, the planet you see down there is called Onyx. It's a Forerunner planet. We were preparing to bring the info we discovered here back to Earth, when the Covenant Armada you just destroyed popped up. As you can see, our fleet was no match for theirs. And on top of that, they had us beat on the ground too, so we had to stay hidden until just now."
"I see. Either way, it's good to have you aboard. I think we should start explaining what's going on."
John explained everything that had happened since he had arrived from High Charity. Kurt seemed surprisingly okay with it.
"Very well, John. My team will assist you in whatever way we can."
"That would be useful. Do you know of any more UNSC personnel existing? Or the locations of any Covenant fleets?"
"As a matter of fact, I have both. Let's head to the bridge."
==Old Friends, New Enemies==
"There." Kurt pointed to a system about two weeks jump from their location. The Canthor system.
"And there."
He pointed to another system about a week from the first stop.
"The first is a hidden UNSC training ground. If the Covenant haven't found it, there's probably thousands of soldiers waiting there. The second is a Covenant recon fleet of fifty ships. They're going to be important, because High Charity moved recently. They have the current coordinates. I think we should head to the training ground first. That way, we will have enough Marines to board one of the ships and get the coordinates if they don't defect."
"I agree." The Grand Commander said over COMM. "We will need overwhelming force if they refuse to surrender, so we can capture them before they jump back to High Charity."
"Then it is settled." Allen said. "We move for Canthor IV, then for the Covenant fleet."
The fleet prepared to jump, and within a week, the second phase of their operation would begin.
...
Orkka 'Regumee could not believe the Commander would ally with the Human filth, let alone betray the Prophets. He took an oath! To protect the Prophets and destroy all that opposed the Covenant! What the Commander was doing was heresy. And, as an SpecOps Commander, his job was to root out, and destroy heresy...
Of course, the personal gain would be good too. Perhaps he would be promoted to Ultra? Or maybe even Field Master? He could only dream of what rewards would await him. Perhaps he would even be offered the Commander's position!
No, he was becoming sidetracked. First, he needed to complete the task. Then, he could ponder what fate awaited him.
He entered the cryochamber of the Assault Carrier Joyous Repentance, and saw the Commander in the pod. All he would have to do was decrease the temperature a bit further, and the task would be completed. He made a quick scan of the room. Nothing. He approached the tube, and before he could open the console, a voice rang out.
"Do not even think of it, Orkka!"
Ssfa 'Jcoree materialized mere inched from Orkka's face. The Elite visibly cringed at the sight of the greatest Imperial Admiral in existence. He was kindest to his men, and cruelest to his enemies. Orkka realized he had just been listed as an enemy.
"Orkka, you fool. Do you not realize that the Commander speaks the truth? He had never lied before! Why would he start now?"
"I do not know, all I know is that he has! Step aside Ssfa, and let me finish my holy task."
"I believe you mean un-holy." Ssfa said as he drew his two green energy swords.
"If you truly wish to end your life this way, Ssfa, so be it." Orkka drew his red energy sword, famous for killing thousands of enemies.
The cryochamber rang out as the two swords sizzled on impact. The two warriors clashed, neither giving an inch. Orkka swept Ssfa out from under his feet. The Admiral fell to the ground, and barely had time to roll away from Orkka's stab. 
Ssfa countered with a quick kick to the face, knocking his younger opponent off-balance long enough for Ssfa to get up. It was then the Admiral realized how outmatched he was. He was still wounded from his fight with Gargantua, not to mention his opponent was younger, and faster, possibly even stronger than he was. Ssfa decided to use his one advantage: His cunning mind.
As Orkka slashed, Ssfa pirouetted to the side, and struck at Orkka's left. Orkka moved to counter, but it was only a feint. The real blow came to Orkka's sword arm, cutting through armor, muscle, and bone. Orkka screamed so loudly that you would have thought he was dying, as his right arm fell to the ground with a wet thwack!
The young Elite was so surprised by this, Ssfa had time to stab his opponent in the chest with the same arm. However, Orkka recovered quickly enough to dodge a third blow, rolled to his detached arm, and grabbed the sword from it. He kicked Ssfa in the chest, and slashed the Admiral across the face, completely deforming the left side of his face. Orkka was more surprised than ever when Ssfa began laughing.
"You fool. I've been hit by a Brute Hammer at Mach 5. You think this is going to faze me?" 
Ssfa struck with lightning-quick ferocity, decapitating his opponent. The young Elite's body hit the ground, finally dead.
The old Elite fell over, still alive, but gravely wounded. He chuckled. 
"Must have done more to me than I thought."
==Infection==
Several days later, the fleets pulled out of Slipspace at the Canthor system, orbiting the former UNSC training planet.
As John looked out of the bridge, he could already tell something was wrong. Very wrong.
The planet was green. But not a lush green you would see in a forest, more of a sickly, disgusting green. John had seen this twice before. And neither time was it pretty for anyone.
"Admiral, don't go down just yet."
"Why not, John?"
John paused, and finally spoke. 
"The Flood are down there."
"Are you sure John?"
"Yes, I'm sure. The Flood are down there. We don't even know if the Marines are still alive. Let me go. I'll scout it out, see if the Marines are alive, and report back."
"Chief!" Cortana chimed in. "You can't go down there alone. If the Marines have been infected, you're going to need some backup."
"Then I volunteer." Kurt said. "I will assist you in any way I can. I will also bring a dozen of my Spartan-IIIs."
"We'll come too." That was Fred, along with Linda and Kelly. "For old time's sake."
"... Fine." John said. "But no more. This is just a recon mission, possibly search and rescue. Our team is big enough as it is, Kurt. Leave your Spartans."
"Aye, sir."
"Then gear up."
At the armory, Blue Team chose their gear for the upcoming mission. John decided to go light, with an M90 shotgun, an MA5C AR, and a M6D pistol as a side weapon. He also picked up two frag and spike grenades in case things got ugly. Fred went with a more heavy setup. He was carrying an MA5B AR, due to it's higher fire rate, and larger clip, a BR55HB SR for longer ranges, and went with four frag grenades. Kelly went with just an M90 shotgun and a lot of extra ammo. She was fast enough to get up close. Finally, Linda went with a Sniper Rifle for recon, and a captured energy sword if the Flood got too close to her. She brought two backup swords, and 4 magazines for her rifle, giving her the lightest setup.
Finally, Kurt went with an MA5K rifle, the weapon of choice for Spartan IIIs, an M90 shotgun, and about 50 pounds of C12.
"Hey, Kurt, what's the C12 for?"
"Quick escapes."
"I guess we'll see what you mean down there, huh?"
"Let's hope you don't..."
Blue Team chose a Pelican from the Launch bay, and descended into the thick green fog that took up most of the planet.
...
As Blue Team trudged through the swamp towards the UNSC encampment, John wondered if the Marines were even alive. Cortana had said that the Flood spores reduced the amount of oxygen in the air. Did it deplete it so much you couldn't breathe? He could only hope he was wrong.
When they got close enough, John could hear gunfire. If someone was shooting, it had to mean someone was alive. He increased his pace slightly, but didn't break out into a run.
Finally, at the edge of the encampment, he saw corpses. Flood corpses. This was actually good. It meant that Marines had been here recently, and they had won. They entered the base to find it empty and devoid of all life. Blue Team spread out across the base, checking in all the buildings. As John exited the mess hall, a message scrolled across his HUD from Linda.
I found something
John and the rest of Blue Team was there in a few seconds, inside of one of the smallest tents there. But they didn't see Marines inside. They saw a hole. John wasn't sure how deep it went, but he couldn't see the bottom. He sent a message to the Antietam.
"Our team has discovered what appears to be an underground cavern. We're going in."
"Very well, Blue Team. Be careful down there. We're detecting thousands of biomasses within 2 kliks of you. None of them are Human."
"We'll keep that in mind."
Blue Team rappelled into the cavern one by one. John was the last in. Just before he entered, he began to hear the ever-growing sound of an unearthly shriek. The Flood were coming.
Blue Team went down double time, and just before they were out of earshot, he heard footsteps approaching the tent...
After a few minutes, they finally reached the bottom. It was pitch black, so they switched to night vision. They found themselves in a large passageway, with two ways to go. One was a dead end, so they went the other way.
As they rounded a corner, they found almost a hundred guns pointing at them.
"Stop! If you move, we'll shoot."
"Relax Marine. That's an order. We're friendlies."
"Holy shit, a Spartan? Five Spartans? We've gotta tell the Lieutenant! Follow us, sir."
The two groups began moving down many winding passageways.
John checked the Marine leader's tag. His name was Cpl. Hank Graves. According to his file, he'd been stationed here for two years now.
"Cpl. Graves, just where are we, anyways?"
"An old ore mine. It was abandoned way before the UNSC took over, but it was pretty fleshed out, we just touched it up and expanded, and it made the perfect fallback point. That's all I really know, sir. You're gonna need to speak with the Lieutenant to find out more."
John heard a faint rumbling.
"Are you still digging, soldier?"
"Aye, sir. We need this to go back pretty far, in case the Flood ever find us out."
"I see."
Finally, they reached the main encampment. John saw tents and fires as far as the eye could see. His first guess at numbers was somewhere around 3,000.
Cpl. Graves led Blue Team to a rather large tent, and told them the Lieutenant was inside. Blue Team entered to find a busy HQ, with men and women at computers and desks of all kinds, and at the back was a middle-aged black man, tagged 2nd Lieutenant Marcus Neal sitting at a desk. He looked up at the Corporal.
"Dammit, Graves, for the last time, I don't care if you didn't find anything, only if you did' fi-- Holy shit. Spartans?"
"Yes, sir. We came to investigate to see if any Marines were still alive here." John explained everything that had happened since the Siege of Last Hope.
"Well, that's probably the best news I've heard in months. Tell the Fleet to come down. I've got a whole lot of wounded to evac. We'll have 'em ready in less than an hour. Graves! Go tell the medics to get the wounded ready!"
"Aye, sir!"
As Graves left, a Private entered the room. He was tagged as one of the diggers on the excavation team.
"Lieutenant Neal? We found something. Something big."
"What do you mean by "big"?"
"You're gonna have to see it for yourself, sir. I'd suggest the Spartans come. We don't know if it's hostile... Hell, we don't even know if it's organic."
The group left the room, and the main cavern, and descended into a long, dark tunnel. At the end, John saw almost 100 Marines gathered around the hole in the wall. He entered the room to find a gigantic cavern, even bigger than the encampment. In the middle of it, was what appeared to be the biggest plant John had ever seen.
"Oh my God." Cortana whispered. "Gravemind."
"I can see that, Cortana. But what is he doing here?"
What am I doing?
Gravemind shuddered, and slowly lurched towards the group.
What am I to do... 
When I cannot leave this prison...
Built to contain me, but cannot hold me?
"Ok. As far as I can tell, Chief, he's pissed. I suggest you stay on his good side."
"I thought you were on one of the Halos?
Another prison...
To contain me...
But I escaped to here. Away from that place... to which I shall never return.
I left unending years ago... before you were created. Before you all were created.
"Ok. You've been here for over 10,000 years. What were you doing?"
I listened...
Through rock and metal and time...
To those who despise me...
He leaned closer to the Humans.
And those who fear me.
Their time's end is near. Your beginning is here. And you shall lead them to it.
My end is near as well. I starve, slowly. Without nourishment for hundreds of years, I will fade away, as will my children.
"Then why are you still alive?"
To warn you. Those who despise me know of your approach. They are watching us as we speak.
"Why would you warn us?"
"Chief, think about it." Cortana said. "The Covenant are his enemies, and they have kept him trapped here, without food. They killed him. He'd want revenge just as much as we would."
Go, and be aware of my warning. Soon, you and the others shall go to war.
One shall stand...
One shall fall.
John vision was blurred, as golden light surrounded him, and as far as he could tell, the rest of the Humans there as well. Suddenly, everything was black.
==Boarding Action==
John and the other Marines from Canthor IV appeared inside the Antietam's docking bay. Medics and an escort appeared to assist the Marines. The Spartans got up and were headed for the Bridge when Admiral-118's voice rang through the ship. 
"John, we have a problem. The Covenant fleet with the data we need is all commandeered by Brutes. As in: They won't defect. What's worse is that they've appeared and are firing on the fleet. We can't fire back or we risk losing the data on board those ships. Get your team aboard a boarding craft, and head for the closest frigate. We've already started the fighting, but we're not doing so well at the moment."
"Aye, sir."
Blue team rushed to a lifeboat, reconfigured to double as a boarding craft, and exited the ship.
As they rushed to the nearest frigate, John saw the hulks of destroyed lifeboats everywhere. Apparently, a third of the boarding forces were killed before they reached the ships.
John, however, was more lucky. The Frigate was pretty distracted as it was, and couldn't afford to fire on just one more boarding craft. They landed safely, and rushed into the interior of the Carrier.
The Frigate was a wreck, with dead Brutes, Grunts, and Jackals everywhere. There was also the occasional Marine laying dead as well. 
Blue Team reached the Hangar, to find a warzone. Brutes on the upper decks fired upon the Marines trapped on the Ground Floor, who were in turn surrounded by Jackals. A Sergeant yelled an order, and frag grenades flew everywhere, killing dozens of Jackals. The squad ran through the nearest doors and reappeared on the second floor. Catching the few remaining Covenant off guard, and cutting them down.
Meanwhile, three ODST Helljumpers took on a Brute Captain, using two spikers. One Helljumper was hit by a round, and his shoulder practically exploded from the superheated metal spike. Four more spikes hit his stomach, and he fell to the floor, dead. The other Helljumpers opened fire, killing the Captain. But at that moment, over a dozen Grunts rushed them, tearing them to shreds.
This entire scene happened in about 30 seconds. John and Blue Team took out the Grunts, and saw several Marines be chased through a doorway by a Brute Chieftan, wielding a Hammer. Blue Team opened fire, but the bullets just ricocheted off of his armor, as if it deflected the bullets. He rushed Blue Team, and Linda drew a sword. She beheaded the Brute with shocking ease.
The Marines met up with Blue Team, along with the rest of the UNSC forces, after securing the hangar.
"Sir, It's good to see some more Spartans. Some of those new Spartans are in the Covenant's bridge, getting the data. We should go help."
The groups carefully moved the the hallways, until they neared the Bridge. Several gunshots rung through the air, and almost a dozen Spartan-IIIs rounded the corner.
"Stop. We've come to help."
"Don't help! Just run!"
"Calm down," Kurt said. "What would scare a dozen of my best Spa- oh. That."
As Kurt spoke, over 100 Brutes came streaming at them, all firing their weapons.
"I see." Kurt seemed to stop for a moment, deliberating something. He then sent a message over FLEETCOMM: "All Marines, get off of the Covenant ships. We've got the coordinates to High Charity, and we are evacuating. I'll hold off the Covenant."
"Kurt, don't. You can't just stay here to die."
"I don't have a choice, John. You need an escape route, and I can give you time to find it. We all die sooner or later John. Personally, I'd like to die fighting."
"... Permission Granted, soldier. Give 'em Hell."
"Hell? That's too good for these sorry sons-of-bitches. I'm giving 'em Hell warmed over!" Kurt pulled out two Assault Rifles and began firing, cutting down the Brutes.
The rest of the group ran, heading for their boarding crafts. Behind him, he heard a massive explosion.
So, that's what the C12 was for.
Blue Team entered their boarding craft, and ejected the ship just before the Allied fleet began firing, plasma and MAC guns tearing through the Loyalist fleet, leaving nothing but dust and echoes.
==Death of a Hero, Fall of a Villain==
Several minutes later, Blue Team finally docked with the Marathon Cruiser Phoenix and entered, to be greeted by 1st Lieutenant and Spartan CJ-007.
"Blue Team, it's good to have you back. Allen wishes to speak with you. Follow me to the bridge and we'll get him on FLEETCOMM."
Once on the bridge, John explained everything. The Flood, the Marine encampment, Gravemind... the death of Kurt.
"I see, John. That news troubles me. I find it hard to believe that a creature as deadly as the flood would die of starvation, but I suppose I have no choice but to believe you. Head back to your bunks and--"
Static. Seconds later, a pulse went throughout the Allied fleet, and in the center, a massive fireball where the Antietam, and Allen should have been.
"Allen! Marathon Cruiser Phoenix calling Supercarrier Antietam. Pick up now!!"
No answer. The Antietam was gone.
At the borders of the Allied Fleet, several Hundred Loyalist ships drifted, at the center, a massive Covenant Supercarrier, almost 10 kilometers long.
On FLEETCOMM, a voice tagged by the Grand Commander as the High Prophet of Mercy rang out.
"Elites! You dare associate, let alone ally yourself with this Human filth?! You shall all burn in the pits of Hell! Your corpses shall parade in our cities, celebrating our victory over you foul heretics! Surrender, and we shall make your deaths quick and only... moderately painful."
CJ immediately responded. It wasn't pretty for anyone.
"You damned dirty bastards! You killed him! You F***ing killed him! I'll blow you to pieces, you bastard!! BURN IN HELL!!!!."
It became very silent for the next moment. John could easily imagine the look on Mercy's face, as he had seen it once before. But he was worried about CJ. This war had affected everyone, and CJ was going to snap any day now.
"Mariah! Aim at the flagship, now!"
"Um, yes sir..."
Even Mariah, an AI programmed without fear, was rather nervous around him.
The Grand Commander opened a comm frequency.
"Calm down, Spartan. If you wish to avenge his death, you shall need a level head."
"And how would you know?!"
"On Earth, you assisted in killing my son."
CJ fell silent, and the Grand Commander began speaking to Mercy.
"Mercy, Truth was never a fan of you. Even with Regret dead, he would never allot you a fleet of this size. You're bluffing."
Mercy hesitated for a moment. 
"Do not underestimate me! My fleet has enough power to blow to smithereens! Your proof is the hulk of a carrier at the front of your fleet." He said with a rather smug grin on his face.
"Why would you hesitate if you were so sure? As a matter of fact, I believe there are less than two dozen ships in your fleet."
Mercy looked as if he was panicking at this point.
"That, my former lord, is all the proof I need. All ships, fire on the flagship!"
Nearly a thousands projectiles of all kinds blasted through space, creating a not-so-miniature sun around Mercy's fleet. With the flagship gone, all but about 5 Loyalist ships remain. A Brute ordered the ships to fire, and several lances of plasma shot across space, destroying 5 UNSC frigates.
A second Allied volley, however, winked those Loyalists out of existence. But at what price?
Johnson walked onto the bridge, and approached CJ.
"Sir?"
"What, Colonel?"
Johnson realized CJ had acknowledged him even though he had been called "sir". He knew Allen's death had hit him. Hard.
"This probably isn't the best time, but I think you should know. With Allen dead and General Parkins still MIA, that puts you in charge, sir."
"Why not you? You outrank me."
"Yes, sir. However, you're still the highest ranking naval officer. And in the UNSC naval officers outrank Corps officers. That means you're in charge."
CJ paused, going over what Johnson had said.
"Very well. I'll do it."
==In memoriam...==
The Allied soldiers were gathered aboard the Phoenix in the commons room. CJ stood at a makeshift podium. He gave a long speech about Allen and Kurt, and how their sacrifice should not be viewed as a loss, but as a victory. They saved humanity, and have given them a second chance to defeat the Covenant once and for all. At the end, there was a funeral for the Spartans among the other Spartans and the others who knew them personally.
At the end of the ceremonies, they all returned to their duties. However, the rest of Hammer Team spoke with CJ.
"I just can't believe he's dead." CJ said. "It just doesn't seem possible. He took on Tartarus and nearly won with nothing but his hands. It doesn't seem right that he died without a choice, without a chance to defend himself."
"That's true." Donna replied. "And that's also why we're fighting the Covenant. They wish us dead, and will use even the most underhanded tricks to bring about that fate. We have to be ready to make sacrifices, including our friends and family, if we want to win this war."
"We should return to our posts." The normally-silent Mark said. "We'll be leaving soon, and we'll need rest before we reach High Charity. We'll need all the strength we can gather."
"I suppose you're right." Cody acknowledged. "Don't worry, CJ. The Covenant are gonna really regret that they killed Allen. This war's just getting started..."
END
==Credits==
*Halo Universe and the Wonderful things in it: Bungie and Microsoft
*Story: MasterGreen999
*Fanon Characters: MasterGreen999 and Grievous797
*Thanks to: 
**Grievous797 for letting me use the Antietam in the story. Sorry it blew up.
**Halo Fanon Community for reading this (I hope 0_o)
**Bungie for creating the richest, most detailed sci-fi universe since Star Wars!
PS: Grievous hasn't helped out much, but I'm planning on having him help out for the third part.