"Admiral McCallister." Gallahad's deep voice came over the com line. "Major Ackerson has returned."

"Good. Send her in." McCallister replied. A few seconds later, Danielle entered the admiral's office and retook her seat. She sat with the data pad containing John-117's complete, uncensored record on her lap as though it were the most mundane thing in the world. "So, I take it you've finished reading our boy's life story?" McCallister asked.

"I have." Danielle replied.

"And?" McCallister asked.

"I understand why you'd think I might find parts of the record disturbing." Danielle replied. "Most people would find the abduction of six-year-olds and the subsequent child soldier training to be a darker shade of grey, to say the least. I imagine that's the reason why ONI is so keen to keep the origins of the Spartans so tightly under wraps."

"Doesn't seem like it phased you, though." McCallister pointed out.

Danielle shrugged. "I acknowledge the program's moral distaste, but I also acknowledge its necessity. The primary failing behind the original ORION project was because, for all their augmentations, the SPARTAN-Is were still just ordinary soldiers. They were all still Human. Dr. Halsey knew that, so she trained the SPARTAN-IIs to become something different from Humans, not only physically but mentally and psychologically as well."

"What do you think she wanted her Spartans to be?" McCallister asked.

"Machines, obviously." Danielle replied without missing a beat. "They were raised from a tender, and more importantly, impressionable age to have an absolute understanding of war and nothing else. And I do mean nothing else."

She then raised her data pad and pressed a few keys. "Records show that the SPARTAN-IIs, John-117 included, routinely exhibited mildly sociopathic tendencies, difficulty with socialization, impaired emotional development….."

Danielle shrugged again as she placed the data pad on the table. "In summary, the Master Chief is one of our greatest assets because he is, at his core, broken."

…..

2203 Hours, March 21st, 2683

Peak 15 Research Facility, Noveria

Pax System, Horse Head Nebula

….

"…..Well, there's something you don't see everyday." N'tho remarked. It was all anyone could say in the face of the insanity that was unfolding before Blue Team. The Master Chief, however, was quicker on the uptake, evident in how he wasted no time in beginning the questions.

"How are you speaking through a dead Asari?" Chief asked the Rachni Queen.

"Our kind sing through touchings of that." the queen replied. "We pluck the strings, and the other understands. She is weak to urging. She has colors we have no names for. But she is ending. Her music is bittersweet. It is beautiful."

"Basically, the Asari is only mostly dead and the queen is capitalizing on that." Cortana interjected, providing a translation for the queen's cryptic words and use of metaphor.

"The children we birthed were stolen from us before they could learn to sing." the queen went on. "They are lost to silence. End their suffering. They cannot be saved. They will only cause harm as they are."

"What do you mean your children are 'lost to silence?'" Chief asked. He was still looking directly at the queen, opting to ignore her Asari hand-puppet. If he was going to talk to this thing, he wanted to at least look it in the eye.

"These needle-men. They stole our eggs from us. They sought to turn our children into beasts of war. Claws with no songs of their own." the queen explained. "Our elders are comfortable with silence. Children know only fear if no one sings to them. Fear has shattered their minds."

"So that's why the Rachni have been acting so illogically." Cortana said in an 'ah-hah' tone. "Leaving edible bodies to rot, hurling themselves into obvious kill zones, it's because without their mother's 'song,' they're incapable of rational thought."

"Don't worry. Your children will be dealt with." Chief said.

"Before you deal with our children, we stand before you." the queen observed. "What will you sing? Will you release us? Are we to fade away once more?"

"I've been examining these controls." Tali chimed in. "This glass enclosure is rigged with acid tanks. Likely installed in case the queen got out of hand."

"Well, what are you waiting for?" Wrex asked the Quarian. "Fire 'em up!"

"Belay that." Chief said as he turned away from the Rachni Queen and walked back up to Blue Team. "We're not executing her just yet. Technically, she's a prisoner of war."

Wrex narrowed his eyes at the Spartan. "Are you stupid?" he demanded. "Your people didn't fight these bastards, so maybe you don't get it. Millions of my ancestors died to put these things down. We can't let them come back."

"I'm with Wrex on this one." Ashley agreed. "I joined the Alliance to protect my sisters from things like this."

"Protection is one thing, but consigning an entire species to death?" Kaidan asked. "Don't forget, she's the last of her kind. We should let the Council decide her fate."

"I don't know." Liara chimed in. "The Council made a mistake once before. They let the Krogan go too far. This is a chance for us to atone. She has done nothing to us. Perhaps we should release her."

"Alright, everyone lock it down." Chief said, recognizing that the discussion was getting out of hand. "We're not doing anythingwith the queen until we find out more about the situation."

"Don't make the same mistake you made on Eletania." Wrex growled at the Spartan. Chief swiveled his head at the Krogan. "You didn't kill Saren when you had the chance, and look how well that turned out."

"This is different." Garrus came to the Spartan's defense. "This isn't one person we're talking about here, this is a whole species. Genocide is one of the reasons why we fought the Krogan….ah….." Garrus's defense came to a screeching halt as soon as he remembered that Wrex was a Krogan.

The mercenary scowled the Turian. "You want to learn about genocide, Vakarian?" he asked in a threateningly soft voice. "I'll take you to a Krogan obstetrician's office."

"I said lock it down." Chief ordered, much more sternly this time, and more specifically directed at Wrex. The Krogan gave him a dirty look, but said nothing else. Good enough for the Chief. He then turned to the Asari the queen was still using. "Wrex does have a point, though. I can't let you go just like that. Not after the Rachni Wars."

"No!" the queen blurted out. "We…..I do not know what happened in the war. We only heard discordance, songs the color of oily shadows."

"Oily shadows?" Chief asked. "What are you talking about?"

"A tone from space hushed one voice after another. It forced the singers to resonate with its own sour yellow note. Then we awoke in this place. The last echo of those who came out from the Singing Planet. The sky is now silent." the queen explained. "If you release us, we would seek a hidden place to teach our children harmony. If they understand, perhaps we would return."

"What do you mean by 'return?'" Chief demanded.

"If we ever return, ours will not be a song of blood. We will not seek to silence you. Perhaps one day, we would seek to sing in time with your own songs." the queen assured.

"Her intentions are peaceful." Liara resolutely stated. "The Rachni aren't wild animals, they're sentient beings. Her race deserves a second chance." Indeed, it sounded like the Rachni Queen would prefer to have peaceful relations with the other races of the galaxy, or at the very least she wants to keep her head down for a while as she rebuilds her species. Either way, another Rachni War was the last thing she wanted.

….Or so the Rachni Queen herself claims. Her stake in this was obvious, as was the fact that she was essentially at the Spartan's mercy. So of course she would say whatever she needs to say in order to convince him to let her go. For all the Chief knew, she's been lying through her mandibles this whole time and she's secretly planning to start a second Rachni War as soon as she has a large enough colony to do it. Liara was right; the Rachni are sentient beings, which means they're no less capable of stabbing you in the back for their own interests than any other species.

Deciding that this ethical dilemma could wait a little while longer, the Master Chief decided to turn his attention on the more immediate objective. The Chief walked over to the control panel that Tali was working at. "Can you access Noveria's security systems from that console?" he asked the Quarian.

"I don't know…" Tali asked. "Why?"

"No matter what we do with the queen, that still leaves her kids to deal with." Chief replied. "I need to know how many of them are left and where they all are."

"I'll try." Tali said as she went to work. "Okay, I'm in. Security systems are down in several key areas….." Tali observed. "But it looks like there's a lot of Rachni congregated further down the mountain."

"That's near the Hot Labs." Garrus said. "Makes sense to me. That's where this whole mess started."

"Alright, here's the plan." Chief said. "Ashley, Liara, Wrex, you three are with me. We're heading down to the Hot Labs to clear out the Rachni. Everyone else, stay here and guard the queen. Don't release her, don't activate the acid tanks, don't do anything until I come back. Is that clear?"

"Crystal, sir." Kaidan said as he saluted.

"The Hot Lab elevator isn't too far from here." Cortana said. "I'll mark it on your HUDs." Chief nodded and gestured the three of his team to follow him down the ramp and through the door that lead out of the Secure Lab.

"Permission to ask a question, Skipper?" Ashley asked as the four of them marched through the corridor.

"Granted." Chief replied.

"What are we waiting for?" Ashley asked. "With the queen I mean?"

"Like Garrus said, this whole mess started down in the Hot Labs." Chief said. "It's where they were studying the Rachni before they all busted out. Way I figure it, it's the best place to see if the queen's story checks out."

"Fair enough." Ashley replied.

…

"You know…." Admiral McCallister said as he leaned back in his chair. "Up until the Master Chief came along, you were in the running to be Humanity's first Spectre."

"That so?" Danielle asked with a raised eyebrow.

"You knew already, didn't you?" McCallister asked.

"I strongly suspected." Danielle replied. "With a record as extensive and successful as mine, it only stands to reason that my name would come up at least a few times during the preliminary discussions." she stated as a fact more than boasted.

"Aye, and you woulda made one hell of a Spectre too." McCallister went on. "But once the Master Chief was found and that rat-bastard Hackett got it stuck in his head to pitch him as our first Spectre, the brass was so busy jazzing their pants at the thought of a Spartan Spectre that they pretty much forgot you existed." he shook his head. "You deserved better than that."

"I don't resent their choice." Danielle assured the admiral. "After all, a living SPARTAN-II? I'd be hard-pressed to pass up such an opportunity myself."

"Don't get me wrong, there's no question about the Master Chief's skills in battle." McCallister said. "But there's a lot more to being a Spectre than just fighting. Spectres are saddled with dozens of other responsibilities that, quite frankly, I don't trust the Chief with."

"You're worried he might abuse his Spectre privileges?" Danielle asked. "Like Saren?"

"Nah." McCallister said as he shook his head and waved his hand. "Saren abused his privileges because he allowed his prejudices and ambitions to get the better of him. John-117 is much too disciplined to make that same mistake."

McCallister chuckled a bit. "No. If anything, the Master Chief has the opposite problem."

…

The elevator dinged before the doors opened. Wrex, Ashley, Liara and the Master Chief all walked into a small, square-shaped room with several chairs, scanning devices, tables full of beakers and other laboratory equipment. Sitting right in the middle of the empty room was a scientist with a stout figure sitting in a chair by himself. The reason for his sitting down became obvious; a wound in his leg. "Are you here to secure the situation?" the scientist asked in a thick Russian accent as the Chief approached.

"Affirmative." Chief replied. He turned to Liara. "Get some medi-gel on his leg." he ordered.

"You must listen to me." the scientist began as Liara knelt next to him and took out her medi-gel. "If we do not contain our mistake, they will drop bombs from the battle stations. You understand?"

"I'm aware of the Code Omega protocols." Chief replied.

"Binary Helix found an egg. It was on a derelict ship, thousands of years drifting." the scientist began.

"It contained a Rachni Queen." Chief replied. The scientist was surprised the Spartan knew that, but nodded.

"After queen lays eggs, they move her to Rift Station." he went on. "They plan to mass-produce Rachni. Create an army. They are thinking that without her, they can raise the babies to be obedient." he shook his head. "Thinking now it was wrong thing to do. Thinking that without a queen, Rachni do not develop properly. Her mind is shaping theirs. These Rachni are uncontrollable."

That seemed to confirm that Rachni grow up rabid without their queen, but that still leaved the queen's motivations and intentions in doubt. In the meantime, there was still her children to deal with.

"Wait a second." Ashley interjected. "Don't you need a male to get eggs?"

"Queens are born carrying the genetic code of their fathers. Eggs are carried away from the colony to hatch alone." the scientist answered. "Queens can lay eggs in hours, and have a colony in days. This is how they spread so quickly."

"I'm done." Liara said as she stood up, helping the scientist on his feet along with her. The scientist hissed and groaned as he put weight on his injured leg, but still nodded his thanks to the Asari.

"This may sound like an odd question." Chief began. "But are the Rachni inherently aggressive or territorial?"

"Not to this degree." the scientist answered. "These Rachni are rabid. If raised by their mother, they would be much more intelligent."

"I know that." Chief replied. "What I'm asking is whether intelligence makes them more or less dangerous. Would they be anything like the Covenant?"

"Hard to say." the scientist replied. "No one knows why the Rachni attacked the Citadel Races in that war. But this queen is not from that era. Perhaps she could be made more open to negotiation than her ancestors."

From the sounds of things, this Rachni Queen could go either way. On the one hand, history depicts the Rachni as a species that is decidedly not peaceful by nature. But the queen hatched by Binary Helix was just an egg during that war, claiming to be ignorant of the hows and whys of the conflict. Thus, she represented a second chance for her race, a chance to do better and learn from the mistakes of the past.

Or so she would claim.

"Can these things…..lie?" Chief asked, all too aware of how ridiculous the question must have sounded.

The scientist was aware of that too, judging from the confused look on his face. "I'm…..not sure." he answered. "Is possible. Once again, they are sentient, not animals. They can theoretically grasp concepts like deception. Why do you wish to know?"

"Long story, I can tell you later." Chief said. "Right now, we should put these things down. How do we do that?" he asked.

"I am thinking that the neutron purge must be set off." the scientist answered. "It creates burst of neutron radiation. Kills everything within the station. Things beyond get genetic damage of varying degree. Arming controls are nearby. All you do is insert the key. Then I will give Mira destruct co-"

He was cut off by a spiked tentacle impaling him in the back and bursting out through his chest.

A Rachni standing behind him squealed in fury at the four before tossing the scientist's body aside. Liara was the first to react, biotically pushing the insectoid away to put some distance between herself and the bug. Ashley, Wrex and the Master Chief then withdrew their assault rifles to riddle the floating bug with bullets. When the biotic effect wore off, the creature collapsed into a bleeding mess on the floor.

"Three, watch that vent!" Chief ordered. "I do not want another one catching us by surprise again." Ashley switched to her shotgun as she jogged over to the vent, pointing the barrel down. Chief then looked over to the scientist's body. No need to check him for a pulse. There was a hole in his chest bigger than the Spartan's fist.

"Take a second and imagine every other Human in Council Space dying like that." Wrex quietly said to the Spartan. Chief turned to the Krogan. "That's what you're risking if you let that thing live."

"Didn't I tell you to lock it down?" Chief asked in reply.

"Chief, I'm detecting a VI terminal in the next room." Cortana said as she slapped a blue arrow on the Spartan's HUD. "Before he died, the scientist mentioned that we would need to give Mira the destruction command."

"He also mentioned a key." Chief added. "Know where that is?"

"Try searching his body." Cortana suggested. "He might have had on it on him when he died." Following the AI's advice, Chief walked over to the scientist's body and checked the man's pockets. He eventually found a small data pad in his left breast pocket. Gesturing the rest of the team to follow him, the Spartan walked over to the other room, which had a large computer network by the far right wall. Chief walked up to the VI terminal and activated Mira.

"Connecting." Mira said. "I have full access to the facility, and am at your disposal."

"Activate neutron page." Chief ordered.

"I'm sorry, but I can't do that without proper code authorization." the VI said.

Chief held up the data pad and read what he presumed to be the code aloud. "Code input: 875-020-079. Code Omega local execution."

"Verified." Mira replied. "Code Omega execution in 120 seconds." With that, the VI's holographic form winked out. A shrill alarm suddenly began blaring throughout the Hot Labs.

Along with the screeches of angry Rachni.

"Code Omega execution in 110 seconds." Mira's voice said over the intercom.

"It's the alarms!" Cortana said. "They're attracting the Rachni here like a dinner bell!" The Chief glanced at the motion tracker and groaned at the sight of dozens of red dots just beyond the door.

"We've got company, people." Chief said. "Seven, get ready to fire a singularity on my mark. Everyone else, assault rifles out and ready."

The Spartan punched the button which opened the door, revealing a room filled with Rachni, both the hulking behemoths and the smaller, roach-like ones. "Mark!" he shouted.

Liara fired a singularity into the midst of the Rachni swarm. The biotic vortex successfully sucked in several of the larger bugs. "Light 'em up!" he ordered as he opened fire, along with Wrex and Ashley. When the singularity faded, most of the bugs collapsed onto the floor, but even more bugs than that crawled out of the vents and charged toward the team.

"Fire in the hole!" Wrex cried as he threw a spike grenade at the Rachni. The flying axe struck one of the larger creatures, piercing its chitinous hide before detonating, filling the air with screeches. However, most of the larger bugs hit by the flying spikes simply pulled the spikes out of their exoskeletons before resuming the charge. The spikes struck deep, but not deep enough.

"The spikes are ineffective!" Liara shouted as she threw out another singularity. "Their exoskeletons are too thick!"

"Good thing I've got these too!" Wrex shouted back as he threw a firebomb grenade at the swirling mass of Rachni, turning it into a flaming vortex of death and agony.

"Code Omega execution in 60 seconds." Mira's voice said as more Rachni popped out of the vents.

"Wrex, toss out more fire!" Chief shouted. "Liara, another singularity! We need to make a path out of here!" The elevator leading out of the Hot Labs was only about forty feet away, but with so many Rachni pouring into the room, it seemed more like forty miles.

Some of the Rachni were sucked into yet another biotic vortex while others were burned alive. "Wrex! Biotic charge to the other end of the room!" Chief ordered. "Clear it from that end!"

"On it!" Wrex shouted as he wrapped himself in a biotic glow and firing off like a rocket. He charged into a Rachni and pumped a few shotgun blasts into its face while it was stunned before switching back to his assault rifle to kill some of the Rachni from behind.

"Code Omega execution in 30 seconds."

"Liara! One more singularity!" Chief shouted. Liara obliged him and summoned another vortex near a large assembly of Rachni. "Everyone switch to shotguns! We're making a run for it!"

The three of them switched to their shotguns before bolting to the other end of the room. Wrex was opening fire on the Rachni pursuing the trio. The three of them eventually ran past him and loaded into the elevator.

"Code Omega execution in 15 seconds."

Wrex tossed one last firebomb grenade at the Rachni before making a break for the elevator as well. With everyone present and accounted for, the Master Chief punched the call button and shut the elevator door, riding it back up. About halfway up, the group heard a loud, booming explosion come from beneath them; the neutron purge most likely. The door opened back up, revealing the ground level again. The four walked back out.

"Alright. I want you three to head back up to the science team quarters." Chief said to the team. "Let the scientists there know that most of the creatures have been killed, so the way out should be clear now. Round them all up and take them to the tram station. The rest of Blue Team will meet you there."

"Where will you go?" Liara asked.

"To go deal with the queen." Chief replied as he walked off toward the Secure Lab.

….

"If you really look at the SPARTAN-II program at large, you'll notice that very few SPARTAN-IIs get promoted past Petty Officer second class." McCallister said. "And there's a reason for that. Like you said, they're machines more than Humans. Specifically, they're machines built and programmed for one specific purpose; to kill. The catch is, that's all they're really good for. That's why not many of them got promoted; the higher up the chain you go, the more things you've got to worry about than just killin' things. ONI decided it was better keep 'em near the bottom, keep the Spartans focused on what they're actually good at."

"That's why you disapprove of the Alliance's decision to sponsor John-117 as Spectre." Danielle stated more than asked. "You felt the post gives him more responsibilities than he can handle."

"Precisely." McCallister replied as he tapped his nose. "It's like making a toaster mayor of the village. If you're looking to make breakfast, he's got ya covered, but good luck cleaning up town square."

"Well, perhaps the Chief has been promoted above his level of competence." Danielle conceded. "But even taking that into account, the advantages of having a SPARTAN-II for a Spectre are undeniable. In addition to an understanding of war, John-117 was raised and trained with an unshakable loyalty to Earth's government. We tell him to jump, and without fail, he'll ask for a precise height every time. He may not be able to think for himself, but quite frankly, that's the whole point."

"Aye, very true." McCallister replied. "That's probably the very reason why so many in ONI were enthusiastic about the idea. Wind's blowing in the Chief's direction, and I've never been one to fight the wind. But if a Spartan Spectre is to truly work in Humanity's favor, certain measures must be taken. Which is where you come in."

"Measures, sir?" Danielle asked.

"Like you said, the Master Chief is more machine than man. And like any other machine, he needs a good tune up now and again. You're going to be his mechanic." McCallister explained. He opened his drawer again and pulled out another data pad, handing it to Danielle. "ONI is scheduled for a series of military exercises with Hierarchy Blackwatch aboard Pinnacle Station. Your unit's been selected to represent ONI."

"And representing Blackwatch?" Danielle asked as she idly read the data pad in front of her. It was mostly a list of rules and regulations for participation in Pinnacle Station exercises; hardly anything she hadn't read before.

"Your old pal, Orex Vidinos." McCallister replied with a smirk.

"….Charming." Danielle deadpanned. The admiral chuckled.

"Don't worry. He won't be your main concern anyway." McCallister said. "That would be the Master Chief. ONI plans to invite the Normandy crew to take part in this exercise alongside your own unit. It will provide you with the perfect opportunity to sit the Master Chief down and give him a performance review. Make sure he has Earth's interests at heart, make sure he's making all the right decisions, generally make sure he's still working as intended."

"Understood, sir." Danielle replied.

…..

The Chief eventually arrived back in the Secure Lab, walking back up to the tank control panel where the rest of Blue Team was. When he arrived, he noticed two things were different. One, there was now a rubber sheet covering Benezia's body, and two, the Rachni Queen's Asari puppet was now slumped against the railing, though her eyes were still on the Chief's. The Asari was likely fading fast and the queen won't be able to use her to communicate for much longer, if at all. The rest of Blue Team straightened their postures in acknowledgement of the Spartan's presence. Even the Rachni Queen perked up a bit, no doubt curious as to what his decision will be.

The Chief walked up to the control panel and weighed his options. Before him lied the potential to either release the Rachni Queen, or kill her. He glanced over to his team, most of their eyes on him, expecting a decision. "…..Go to the tram station." he ordered them. "I'll catch up in a minute."

Kaidan nodded and wordlessly ordered the rest of the team to follow him to the tram station. Within minutes, the Spartan was now all alone with the queen. He wasn't entirely sure why he ordered the others to leave the Secure Lab. Maybe he just didn't want any eyes on him as he deliberated this. He was under enough pressure as it was.

The Master Chief was familiar with the Rachni Wars. It started when the Salarians discovered and activated a dormant mass relay, which lead to the Rachni's home territory. The space-faring insectoids wasted no time in establishing that they weren't interested in peaceful coexistence with the other races and began expanding their territory by moving through the relay and attacking Citadel worlds.

All attempts to contact the Rachni to negotiate a ceasefire were futile. The hive queens resided deep beneath the surface of their homeworld Suen, which not only had an atmosphere that was toxic to most non-Rachni species, but was tidally locked to boot. Even if contact with the queens could be made, it was quickly learned that the Rachni spoke in a language so complex, that mutual communication was all but impossible.

After nearly a century of fighting a losing war against the Rachni, the Salarians discovered and uplifted the Krogan, whose introduction marked a turning point in the conflict. The Krogan were not only able to reclaim all of the ground lost to the Rachni, but were even able to drive them all the way back to Suen. Even with their backs against the wall, the Rachni refused to stop fighting, which left the Krogan with no other choice but to obliterate their hives with weapons of mass destruction.

In summary, the Rachni were to the Citadel Races as the Covenant was to the UNSC; a ferocious, relentless enemy who never once showed an interest in diplomacy. Even after it became clear in the final battles of the war that the Krogan had them dead to rights, the Rachni opted to go down swinging rather than surrender.

With all this in mind, the answer to this dilemma was obvious to the Spartan's strategic mind; pour on the acid.

But this queen had been doing something that the other queens never did; communicate with him. Granted, she had to do it in an indirect manner and her vocabulary made her hard to fully understand, but the dialogue happened and she was clear enough for the Spartan to gauge her alleged intentions. She was at least willing to talk to the Spartan, which sounds like more than the queens of the past ever did.

Or maybe that's just what she wanted him to think. The Master Chief still hadn't ruled out the possibility that she was lying. He couldn't believe that she wouldn't start trouble just because she said so. In fact, it wouldn't even take her very long to start trouble if she wanted to. According to the Hot Lab scientist, a single queen could have a whole colony up and running in a matter of days, even without a mate. She would easily have an army of thousands at her command before the year was out.

He couldn't risk history repeating itself. He had to activate the acid. He punched in the relevant commands and then…..

He was about to press execute when a realization stopped him. A realization that almost trumped every logical reason there was to kill her.

She was the last of her kind. If he killed her right here and now, that would be it. Never again would the galaxy see Rachni. A whole sentient species rendered extinct by his hand. Genocide.

Which was once the Covenant's own goal.

The Spartan shook his head. This was different. The Covenant's genocidal campaign was fueled by dogmatic hatred. This was a simple matter of survival. The Rachni's destruction wasn't the 'Will of the Gods,' but simply eliminating a future threat before it got out of hand. Still, genocide. The word kept popping up in his mind, nagging him. He tried to assure himself that, grim as it was, it was necessary. The Rachni were as bad as the Covenant, and if this were somehow the Covenant he was dealing with, he would have punched in the kill command without hesitation.

…..Would he?

The only reason the UNSC never tried to commit genocide on the Covenant was because they could never get into an adequate position to do so. The Covenant had Humanity boxed in from start to finish. The last hope near the end of the war was Operation: RED FLAG, whose goal was to kidnap a Prophet, forcing the Covenant to negotiate a ceasefire. Peace was the ultimate goal of that operation, because war was no longer considered a feasible option.

But suppose that, somehow, that changed. Say the UNSC devised some sort of plague that would not only halt the Covenant's advance, but wipe them out entirely. Every elite, every brute, every jackal, grunt, hunter and drone. Every last one. Every man, woman and child, combatant or otherwise. Dead and gone. Wiping out one species to save your own. Would the Master Chief do it then?

Once upon a time, he would have done it, without question. But after knowing the Arbiter, knowing N'tho, realizing that the Sangheili and the other Covenant races were people, no different from Humanity? He honestly wasn't sure.

Chief shook his head and hit the cancel button, resetting the controls. Maybe Kaidan had it right all along. Maybe he should just let the Council decide the queen's fate rather than try to take matters into his own hands. This was clearly above his pay grade anyway.

But he knew what would happen if he did that. The Council would likely come to the same conclusions his tactical mind came to; letting the Rachni Queen live was simply too big of a risk. They would likely order her execution and her species would still go extinct, the only difference being that the blood of an entire race wouldn't just be on his own hands.

Or maybe the Council won't kill her. Maybe they'll try to do what Binary-Helix tried to do; control the Rachni. Study them. Which meant that the queen and her children would spend the rest of their lives in glass tanks just like this one. Somehow, that didn't seem any better than extinction.

This honestly felt like yet another one of Dr. Halsey's tests. Would you commit genocide on one species to prevent a possible one of your own? It sounded like exactly the kind of philosophical scenario she'd propose to her Spartans to test their morals.

What would she want him to do in this particular scenario? Would she do everything in her power to keep Humanity safe from any and all possible threats, as she always had? Or would she believe that the cost in this instance was too high?

John remembered the last lesson he taught her. The value of a single life. How important it was to save every life you could.

….

"I'm serious about this, Danielle." McCallister said. "You need to make it clear to Spartan-117, in no uncertain terms, what our interests are and what we expect of him. We have to keep a short leash on him. We can't trust him otherwise. You see Danielle, when you're a Spectre, many choices lie ahead of you. None of them are easy."

He leaned forward in his chair, wagging a finger at Ackerson for emphasis. "And you can't trust a broken man to make the right choice."

….

John reached a decision. He knew what he had to do now.

He typed in the commands and hit the execute button.