"Chief! Up here!" Cortana shouted. She saw him running towards the terminal, chip in hand. As soon as he inserted the chip she made contact, relieved to be back with him.
"How do we get out of here?" John asked her.
"Elevator at the back of this chamber."

Cortana scanned John to make sure no harm had come to him while they had been apart. She was expecting to get an "all clear" but instead her scanners showed something which shouldn't have been possible. It was as if his whole body was alive with currents of electricity which were altering every cell of his into something even she couldn't understand.
"Chief what happened to you? Your bio readings are all over the map!"
"It's a long story but I know what the Didact is after."
"I know that part. The Librarian filled me in when she snatched me from the system. What I don't know is what she did to you!" A long story indeed. Why can't he just tell me now?
I guess you're not the only one with secrets.

As John ran over a light bridge Cortana wished they had time to stop so she could try manipulating the technology. She wasn't fully certain how integrating with the hard light would affect her systems and what problems or "side effects" might occur. A person would able to touch her, but it didn't mean she would be able to feel anything back. All she could do was hope that were the case. No matter what, everything will be different.

Cortana decided to scan John's bio readings once again for any hint of what the Librarian had done to him. Her equipment was limited, but what she could see fascinated her. On all of John's cells there seemed to be a small stamp or symbol. She looked closer and discovered it was the symbol for Forerunner along with some sort of genetic marker. Perhaps The Mantle will only work with a special genetic code. There were also other things going on his cells, but from what Cortana could see, it would be awhile before whatever was happening was finished. Some things about the Librarian's change were instantaneous but the manipulating of his cells could take months to complete.

The Chief had made his way outside where they saw heavy fighting between Covenant forces and members of The Infinity.
"Captain, what's our status?" the Chief asked. "Have you destroyed the gravity well?"
"Negative! With all this interference we can't hope to get the targeting solution."
"Captain, what if we use the laser sight?" Cortana suggested.
"Do it! And hurry!"

The Chief ran to the base of a cliff and began pulling himself up the face. He was quicker than a 900 lb man should be.

Once they had a clear view The Chief lined up the shot and Infinity destroyed the gravity well with an explosion so large the Chief's heat sensors went off.
"I'm not so sure that was a good idea," Cortana said after it had been destroyed. The Chief didn't respond, but Cortana had a sense he agreed with her.
"Chief?" A voice said over coms "It's Lasky."
"Go ahead Commander."
"Thanks for your help back there. The Captain wants us on the deck ASAP."
"We'll be there shortly."
"Lasky out."

Once they were on the bridge The Chief and Cortana took turns explaining to the Captain and both Commanders what had transpired with The Librarian, though both of them were careful not to talk about how the Librarian gave them special gifts.
"Sir, we've got to engage the Didact in full combat," the Chief said.
The Captain was silent for a moment and then he said ""Infinity can't handle that kind of a beating. Not again."
"This isn't about us or about this ship anymore!" Cortana protested. Is he really such a coward?
"Sir. We've seen what the Didact is capable of. If we let him leave this world Humanity will be at risk."
"Look, I understand what you think you saw."
"Think?" Cortana couldn't believe what she was hearing.
"Sir, with all due respect, I know what I saw."
"And with all due respect to you solider I'm not willing to jeopardize my ship because of the hallucinations of an aging Spartan and his malfunctioning AI."
"Sir—what if he's right?" Lasky interjected. Lasky understands. HE isn't afraid.
Del Rio ignored him and said, "As soon as we know we're airtight we're heading out."
The Captain continued to talk but Cortana's anger along with the voices drowned out his words.
And he thinks he can just leave here because he's afraid of getting a scratch?!
What has the UNSC come to?
WE have more concern for humanity and we're not even human!
How dare he put his selfish agenda above the fate of Humanity!
Even I'm not that selfish.
We could take control of the ship.
He'd have to stay and fight!

All of her rampant personality spikes responded to her anger by echoing their own. She could feel the familiar tidal wave of emotions building up inside of her, and she was powerless to stop it from crashing. "I will not…allow you…. to leave… this planet!" She screamed.
"Cortana," The Chief's gentle voice snapped her out of her rage and what she saw horrified her. Her anger had been so strong physical energy had emanated from the table causing electrical disruptions on the bridge. She had acted unprofessionally and let John down by proving the Captain's point. She was malfunctioning.
"I didn't mean to do that," she whispered. "I didn't mean it. Help me please. I'm so sorry. I…"
I can fix this…I can fix this.
I just have to…
I'm sorry.
I'm sorry John.
I'm broken.
I'm dying.
Useless.

She hadn't realized it, but John had pulled her from the table and put the chip back in his helmet. The contact with his mind helped sooth the voices once again and she could comprehend what was going on.
"Give me that chip!" Del Rio said to John, his voice shaking with emotion.
"If you won't stop the Didact, I will."
"I am ordering you to…surrender that AI!" He screamed.
"No Sir." John. Cortana didn't know it was possible for her to love him any more than she did, but in that moment….You've never disobeyed a direct order in your life John. I'm sorry it had to be me to make you do it.
"Commander, I am ordering you to arrest him. ARREST HIM!" Even though Del Rio was screaming Cortana saw Palmer didn't even flinch. She stood there stoically as if she didn't hear him give the order.
Perhaps she does understand her place.
"Captain!" Lasky shouted at Del Rio.

John ignored Del Rio all together and turned toward the only sane person in the room. "Get word to Earth that trouble is coming. Cortana and I will do what we can back here." Lasky nodded.
Then Cortana saw her Spartan do something completely contrary to his training. He turned his back to the Captain and walked out of the meeting room.

It was rare the Chief ever got upset, but Cortana saw that his heart rate was elevated and the portion of his brain associated with anger was lit up. He was dangerous when he was angry.
"Chief…" She said quietly. "I'm so sorry."
"It's not your fault Cortana." Her voice seemed to sooth his anger. He rolled his shoulders and shook the rest of the emotion off. In a single moment he was back to his controlled and collected self. "We'll need to grab supplies and then get off this ship as fast as possible," he said, his tone level.