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Ok, be forewarned! The bulk of this contains direct spoilers for the Halo novel First Strike!
...
Perhaps the ground team is gone, due to Enkidu, who could be in the Jealousy stage of rampancy.
Perhaps Enkidu, once wild with the Lebanon and her crew, has been introduced into the urbanity of a Forerunner structure, and now resents it.
Perhaps Enkidu sent the distress message to the Covenant.
And I tracked down what people have been associating the Covenant ship with in their memories. The Covenant cruiser Sword of Justice would probably be of the same fleet as the Ascendant Justice, under the Prophet of Justice. The Ascendant Justice is the ship that John & co. captured after the destruction of Halo.
Now from the BLAM! you might've been waiting for. A few quotes, starting on page 63 of the novel Halo: First Strike :
The Chief Halted and killed his external speakers so he could speak freely. "Problem?"
"No. A lucky break, maybe. Look to your left and down twenty centimeters."
The Chief squinted and noticed that a portion of the wall extruded into a circular opening no larger than the tip of his thumb. "That's a data port... or what passes for one with the Covenant Engineers. I'm picking up handshake signals in shortwave and infrared from it. Remove me and slot me in."
"Are you sure?"
[...]
"When have I not been sure?" She snapped.
The Chief could sense her impatience through the neural interface.
He removed Cortana's data chip from the socket in his helmet. The Chief felt her leave his mind, felt the heat rush back into his head, pulsing with the rhythm of his heart... and once again, he was alone in the armor.
[...]
Cortana was built for software intrusion. She had been programmed with every dirty trick and code-breaking algorithm the Office of Naval Intelligence had ever created, and a few more tricks she'd developed on her own. She was the ultimate thief and electronic spy. She slipped into the Covenant system.
[...]
"How is it?" the Chief asked.
Now the element of surprise was gone, and the system's counterintrusion systems were running on high alert. Something else prowled the systems, now. Delicate pings bounced off the edges of Cortana's presence; they probed, and withdrew.
It felt as if there were someone else running through their system. A Covenant AI? There had never been any reports of alien AIs. The possibility intrigued her.
[...]
A tickle of feedback teased through the data stream.
Cortana locked onto the source of that feedback, listened, discerned a nonrandom pattern to the signal, then cut off contact. She had no time to play hide and seek with whatever else was in this system.
[...]
She sent a blocking countersignal along the connection where this "other" was trying to contact her.
[...]
Cortana picked up increasing communications bandwidth between the flagship and the cruisers. Reports of the invaders -- a cry for help -- a warning to be relayed to the home world. There were references to the "holy one," and those messages had what she considered amusing attempts at encryption to keep them secret. Curious, she had to investigate what the Covenant thought important enough to hide.
[...]
The other presence in the system tried to shut the pumps off. She blocked that signal and assigned a new code to the security systems: "WE REGRET TO INFORM YOU."
She heard the other AI scream, an echo of an echo that revertebrated through her processors. She knew the sound--familiar like a human voice, but terribly distorted.
[...]
Cortana was annoyed. She had let the Covenant AI--for that's what this other presence in the system undoubtedly had to be--trick her. She had gone straight for the simple lockdown of the NAV systems. She never performed a thorough systems check[....]
[...]
Cortana swore that when she caught this guerilla Covenant AI, she'd erase it line by line.
[...]
Cortana emerged from her cocoon of concentration and immediately sensed the electronic presence of the other near her, monitoring her slipspace calculations. It was practically on top of her.
"Heresy!" it hissed and then withdrew ...and vanished.
[...]
"Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel-Infidel--"
"That's quite enough of that," she said. "You and I need to come to an understanding." She reduced the memory pathways, peeling the Covenant AI apart code layer by code layer. "This is my system now."
While an operational Covenant AI would have been a prize for ONI Section Three--this particular Covenant AI was too dangerous. She could not allow its existence to continue.
"Do what you will-wil-willwill," it screamed, "I go to finally to my heaven reward paradise final-finalfinalinfinityinfinityinfinityinfini-AT NONCOPYSTATE."
Cortana's curiosity over this odd proclamation would have to wait--forever. She tore the AI apart, erasing, recording the Covenant code structure even as she destroyed it. This was analogous to a dissection, and she did it quickly, efficiently, and without remorse--until she found the AI's core code.
She halted
She almost recognized this code. The patterns were maddeningly familiar. No time to ponder why, though. She recorded it and then wiped the original. The Covenant AI was gone, its bits safely hacked apart and stored for future research. Provided, of course, Cortana had a future.
[...]
Small portions of the alien software looked like her. The odds of such parallel evolution in computer science seemed improbable. It was almost as if it were her code... only copied many times, each time with subtle errors introduced by the replication process.
Could the Covenant have captured a human-made AI, copied it, and then used the result in their ships? If so, why had there been the need to replicate the code so many times? And with so many errors?
[...]
[...]She ran a trace on the origin of the copied pathways of the alien AI, and found its replication routine. This copying code was extremely convoluted; in fact, it took up more than two thirds of the Covenant AI's processor--memory space. It was dark with functions that ran deep to the core. It spread dendritic fingers through the system, like a cancer that had metastasized throughout the AI's entire body.
She did not understand any of it.
These are the relevent sections of the text, I believe. There is more to what I've quoted here, but I really did not wish to retype that much of the book. (And I hope Mr. Trautmann will forgive me for quoting as much as I have, here.)
The conclusions I have reached are thus:
1) Enkidu has indeed been changed by his contact with the Forerunner system. He has not been taken over, however, and it is possible that the reason his origin is listed as unknown is that he's broadcasting from within the Forerunner structure, using the structure's comm. systems rather than the human comm. systems that he had been using.
2) Enkidu has gone rampant and, as of the "How I Spent Your Summer Vacation" section, is in the Jealousy Stage of rampancy. He is therefore highly dangerous and very much capable of destroying his former friends of the Human crew. One way he might ensure this would be to call in a Covenant fleet to smash the already crippled Lebanon.
3) Enkidu is not captured by the Covenant; rather, he joins them willingly, probably from the head trip of suddenly being a god-like being to be worshipped. He is, in other words, a new spin on an old "friend" of ours...
So... we have Leela (Cortana) and Tycho (Enkidu)... but where's Durandal?
~Socrates
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