Updated (3/12): Author Notes: So, after nearly a year, I decided to go back through and reedit the fic. Most of the sections are basically the same-minor dialogue tweaks, random spelling corrections, date changes, etc. However, there are some major changes in certain sections. Most significantly, there is an entire new part entitled, "Playing Defense" which helps tie in certain plot aspects especially with the sequel I'm planning to write. The end of "Let's Get This Show on the Road" and the beginning of "Pushing the Boundaries" have been completely rewritten.

Original Author Notes: First things first, this story is a major AU. Everything takes place on Earth (though in the same time frame). No aliens or space battles here. If that sort of thing bothers you, then this isn't the story for you. There are about a thousand or so nods to Eric Nylund's incredible "The Fall of Reach" novel. And a huge thank you goes to the good people at Halopedian.

Secondly, this story IS finished. I plan to post a new section every other day.

North America, Reach UNSC Military Complex,
Omega Wing-Section Three secure facility
December 12, 2551

Today was the day that would mark the change in the fight against the Covenant.

Today Cortana would be partnered with Spartan-117.

It had taken three months for ONI and High Command to approve the armor upgrade for the Spartan. The opponents argued that advancement was expensive and risky; if it failed, the UNSC would be unlikely to recover from the investment. But, after hearing both her and Halsey's persuasive testimonies, the admiralty, led by the influential vote of confidence from Lord Hood, finally green-lit the project.

Unlike the slow moving bureaucracy of High Command, once the permission had been granted, Cortana and Halsey had worked quickly to move the process forward. It had taken Cortana less than a half a minute to decide on her Spartan counterpart and nearly as long for Halsey to agree. The paperwork had been rushed through and Spartan-117 had been removed from his current team and transferred to Reach.

Now, Cortana was getting ready to do her part to complete the project.

The Master Chief was in the lab with Halsey already, getting accustomed to the first set of upgrades on his armor: a new shielding system, an onboard data storage unit that rivaled most ships in the fleet, and an advance HUD.

But that was nothing compared to the second half of the upgrades, she thought with a smirk.

"Cortana." Halsey's voice cut through her thoughts. "We're ready for you now."

She looked at her reflection in the window and straightened her short, black hair, pulling it away from her face. Satisfied, she turned away and walked inside the doctor's lab.

"This is Cortana," Halsey said, stepping to the side as she entered the room. "She is part of the upgrade to your armor I mentioned earlier."

Cortana took in the sight of the Master Chief before her. He had been fitted in his armor, though he hadn't yet put on his helmet. His short brown hair matched his cocoa colored eyes. There were several scars on his cheeks and neck, a testimony to the amount of time he had been fighting the Covenant. He looked serious, unshakable. He was every bit the professional soldier Cortana believed him to be.

There was no doubt that he was the right choice.

She watched as his eyes flickered between her and Halsey, no doubt noticing the similarities between the two women.

She stuck out her hand for him to shake. "It's good to meet you, Chief."

"Likewise, ma'am," he said as he shook her hand.

"Cortana," she corrected.

"Cortana," he repeated uneasily. He looked at her ONI issued uniform for any signs of rank, but found none.

"I'm a fourth generation AI," she said as way of explanation.

The Chief looked her, confused. "But you're human..."

"I am," Cortana answered, amused by his awkwardness. She turned to Halsey. "You didn't tell me how observant he was."

She noticed how the Spartan stiffened at her dig. She was tempted to apologize, but decided against it. He would have to adjust to her personality if this partnership was to work. If he was expecting someone who fit the UNSC mold the way he and his fellow Spartans did, he was in for a bit of a surprise.

"You'll have to forgive, Cortana. She's a bit more...high-spirited than you," Halsey quickly interjected. "She is a human-AI hybrid, the first of its kind. This allows for her, when working with your armor, to be in two places at once. We're going to implant a shard of Cortana's matrix chip into your neural interface, John. Her core programming will be able to communicate directly with your armor and its data while allowing her to remain mobile. We believe that with the two of you working together, it will allow for us to access more of the Covenant databases, to try to get ahead of them."

Cortana frowned at the mention their long-standing enemy. The Covenant, the zealous cult that had started off so small nearly forty years ago had grown into humanity's biggest threat. They controlled nearly seventy percent of the world's land mass and dominated over two-thirds of the world's population. Those that didn't join their forces were killed ruthlessly and mercilessly.

The UNSC, the United Nations Salvation Collation, were the only major force in opposition to the group and even they were fighting a losing battle. Over the years, the UNSC lost dozens of strongholds to the Covenant. The only promising signs that the UNSC would ever be able to stand against them were Halsey's Spartans. Now, with Cortana joining the fight, humanity had its best chance of stopping the Covenant from gaining any more ground.

The Chief looked at Cortana with grim smile, bringing her thoughts back to the present. "Understood, ma'am."

"We're going to proceed with the coupling process. John, please finish putting on your armor and have a seat," Halsey instructed.

He grabbed his helmet from its position on the metal table and placed it over his head. When the locks clicked into place, he raised his visor. He was still watching her closely, Cortana noticed.

She watched as the Chief sat in the large chair, allowing Halsey to have access to the back of his armor. She wondered if he understood what the link would mean for him, that no matter where he was on the planet, a part of her would be with him.

She stood in front of John and flashed him an encouraging smile.

He looked at her blankly.

Briefly, she wondered if he was perhaps a little too rigid for her personality.

Cortana turned around to face the doctor who seemed unconcerned with the Chief's stolid behavior. She trusted Halsey. The doctor wouldn't risk the project failing. If she thought there was going to be a compatibility issue, she would have brought it up to the AI before getting this far.

"Look forward and do not move. I will tell you when the procedure is complete," the doctor said from behind him.

"Are you ready?" Halsey asked, glancing at Cortana.

Cortana nodded. According to the simulations they had run, she should feel nothing more than a faint energy drop as the shard reconnected with her matrix chip inside her body. Once the shard was recognized by the Chief's armor, it would allow her to have a direct window to what the Chief saw.

She watched as Halsey carefully removed the shard that was suspended in a matrix chip from its cylinder-shaped holder. She heard several clicks as the chip slid into place in the Chief's armor.

She felt a tug in her consciousness as the shard reached out to connect with her neural lace. "All right, I've got it," Cortana said. "Activating MJOLNIR interface now."

She stumbled slightly as the huge influx of data came roaring into her matrix. Quickly, she created a buffer between her and the Chief's armor, allowing the data to flow in at a more easily digestible rate.

Halsey looked at her questioningly, but Cortana waved off her concern. She would be fine.

She switched her subroutines and transferred her primary system into the shard. It felt strange for her to be confined in the small matrix chip after being in her host body for the past several months. But, she adapted smoothly and accessed the armor's systems. "I'm in." Cortana's voice came from his helmet speakers.

When the Chief turned to face the human sitting next to him with an inquisitive look, she waved. "Please don't be surprised at my ability to do more than two things at once," she quipped.

"Excellent," Halsey murmured, taking notes. "And are you getting the readings from all the armor's systems?"

"Yes," Cortana said, distracted. She accessed his vital signs during the procedure. He had nearly lost consciousness when the shard was implanted into his neural lace.

Had they missed anything else in the simulations?

"She's in my mind?" The Chief's voice pulled her back into the discussion.

"That's up for debate," Cortana said, transferring her main systems back to her matrix chip and allowing the normal subroutines to work in the shard. "My subroutines will transfer your neural impulses and transfer them directly into motion. So, in that regard, yes, I'm in your mind."

"But," Halsey interjected, "she will only be able to perform those actions when you are in your armor. When you are not in it, the shard will be no more intrusive than any other part of your neural lace."

The Master Chief shifted his gaze to Cortana briefly before looking back at the doctor. "I feel a hum in the back of my head. Is that normal?"

Cortana exchanged a glance with Halsey. Yes, there was a chance that he would "feel" her presence, but the doctor had assumed the sensation would be minimal at most.

The doctor looked unperturbed. "That is to be expected. When you're not in your armor, Cortana's chip will be nothing more than a hum in your subconscious, like your heart rate or your breathing patterns. It might take time to adjust, but soon you won't even know she's there," Halsey assured him.

Cortana raised an eyebrow at the doctor, surprised at how confident she seemed. While it was true that they had no evidence that there wouldn't be any lasting side-effects of the link between the two of them, the truth was she and the Chief were entering into untested territory. No one knew what the long-term effects of the connection would be. Not even Halsey.

"Now, if the two of you would follow me, High Command had arranged a little...test before they give you the final green-light," Halsey said, leading them out of the medical room.

Cortana frowned slightly. Why hadn't she known about this?

"And you thought giving up a thirty-second advance warning would help the cause?" Cortana asked sarcastically.

Halsey didn't reply to her comment. She picked her tablet off the desk and led them to the door. "Follow me."