I don't have a lot of time right now. As you've seen by now, this landing site was a complete disaster. The Pfhor and Renegades are already deep in combat with each other, and of course we ended up smack in the middle of it all. What you found last night at that Renegade construction yard, and what was corroborated by the invasion of their intelligence center earlier, was that the Renegades have been harvesting materials from the Atreides wreckage ever since it crash-landed. Because the Atreides was a top-secret research vessel, they are in possession of extremely... volatile knowledge and technology that we can't afford to surrender to the aliens.
Like Phoenix. Phoenix was a new piece of hardware that was (theoretically) incapable of reaching full rampancy due to physical limitations in its neural network. This sort of inherent unreliability in earlier AI systems may have been why Tycho isn't as much of a danger to us as he could be in the hands of the Pfhor.
Anyway, AI technology is probably our single biggest advantage over our enemies. Unfortunately, our attempts to contact it through the remains of the ship have failed. We're completely unable to detect whether or not Phoenix is still functional or intact. Therefore, you're going to have to find it yourself. I had teleported you into the site as closely as possible, but with the mess of the wreckage, you may have to get... creative. When you reach the AI housing chamber, confirm the status of Phoenix and head to the nearest terminal for exfiltration.
The status of the Atreides is peculiar. Large sections of the ship are entirely intact. This is not surprising; UESC ships in general are exceptionally massive and sturdy. However, other sections of the ship have been completely decimated, as you have certainly seen by now. From what you discovered, we already know the A'khr have been harvesting materials to craft their own technology. But their use of materials is not exactly... methodical. What has happened to the rest of the ship? What else are the Renegades doing with it?
This is a complete nightmare. See, this is what ultimately happens when the UESC sends a research vessel when a fully-staffed warship like the Hydra would have been a better fit. The security guys are completely out of their depth here, so I've been pulling most of them back. I'll keep a few squads around to specifically support you, but you have to promise me -- keep them alive. You're the only one who can make it through this mess, and hopefully turn this from a complete slaughter into a vague success.
Phoenix's housing chamber is just through here. By monitoring the local troop movements, I can guarantee that the Renegades are going to make their last stand in the area just behind this wall. I've brought in the last couple squads still in this area to try and reinforce you, or at least draw off enough troops to let you make your way through. There's got to be an access point inside the Phoenix chamber, so when you find it, we can move out.
Phoenix is gone! I guess I shouldn't be surprised by that. The AI housing cell is particularly damage resistant, for obvious reasons, and yet some parts of it have been completely torn away. It wouldn't surprise me if the Renegades had taken Phoenix away. This chamber holds -- well, it held -- the main personality cells. What would they have done with them...? In any case, it is absolutely vital to find Phoenix, and destroy the cells if necessary. Besides the knowledge within the databanks, we can't afford to let the Renegades have competent AI technology. But first, while we're here, we also can't let the Renegades (or, maybe more importantly, the Pfhor) keep rummaging around the ship's innards. As I said before, the UESC Atreides is a top-secret research ship. We'll have to destroy it.
The teleporters in the room behind this wall will take you to the residential divisions in the center of the ship. Also in this sector are the mechanisms to run the self-destruct sequence. This is a complicated procedure that can only be done manually, and presumably the staff onboard were routed before they could pull it off. I'm going to be busy with the Istanbul crew. They've suffered heavily. I'll leave you in the care of the S'pht'Kr and whatever few men I have that are still in condition to fight.