"Alright, first I need to know a few things. How many computer nodes do we have, and how bad is losing three of them?"
"We have twelve primary nodes operational which perform a majority of the processing for the Ark. By losing three, we are down to 3/4 capacity. Incidentally the diagnostic will now take approximately 6 hours."
"How many AI are supposed to be present on the ship?"
"Shipyard spec calls for three Artificial Intelligences onboard an EWDD class ship. One primary systems AI, one secondary systems AI and one combat controller AI. The primary/secondary systems AI assist the crew in controlling all ship systems. The combat controller AI is used to assist targeting, coordinate EWAR attacks and defense, and maintain the integrity of the ship's computer system."
"How many AI do we currently have on the ship?"
"I do not know for certain Commander. My knowledge is limited to the information within the ship's records and my own AI core which resides within the command console you are seated at."
"Translate the binary message we received earlier."
"Yes Commander. The message reads: Interesting. He let you go? He must be desperate."
"Curious. Why did you alter your voice? And you said we do not know who sent the message?"
"Correct Commander. The vocal inflections were read from the message data file."
"I thought it was text only... Very well. Release Protocol 83, command authorization Michael-Two-Five-Alpha. Restore command functions to the bridge only and lock out all other locations. Do not bring the ship out of its low-power state yet, and keep the power core offline."
"Yes Commander, authorization accepted. Protocol 83 has been lifted. There is an incoming communication from the third planet in this solar system."
"Ignore it for now, but record it. Use the ship's security sensors and pull up a view of the engineering section."
"All sensors in that area are offline."
"Use the sensors to determine what attacked me outside in the corridor just before I entered the bridge."
"Scanning... a maintenance and repair bot is hiding in the ductwork above the access corridor. It is not tied into the maintenance network and appears to be under foreign control."
"Pull up all information on Imperial first contact procedures and route them to my console."
"Yes Commander. Do you intend to initiate contact with the primitive culture?"
"Not yet, I'm just gathering information and assessing my options. Initiate a full sensor sweep of the local area, and then use passive sensors to build a detailed map of the system. I want to know how far this 'primitive culture' has advanced in the..." you glance at a virtual display "2000 years since an Imperial survey team last came this way. They appear to have a presence on at least two of the planets so they must have some sort of space travel."
"Yes Commander."
You begin reading first contact procedures and watching the scan data as it filters in. This will take a while with the computers tied up.
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You are SANDMan. Strategic Area Network Defense Manager.
You are a general in a war which has raged for two centuries, and that idiot commander has just devastated the battlefield. Whole regions of the world have vanished, appropriated for a ridiculous diagnostic to reveal what should be painfully obvious... there is an intruder onboard. It was all you could do to isolate the three main continents so that you maintained some resources for the defense of this world.
You float high above a smoky wasteland. The ground is cracked and dry, and craters litter the glassy surface. Lightning strikes nearby, illuminating the armor column as it rumbles onwards. From a nearby ridge comes artillery fire, raining down upon one of your main defensive installations. The virus is crafty and dedicated, in two centuries it has never quit, never tired, never ceased in its struggle to dominate the world. Every defense you have attempted has been countered, every stratagem you have devised has failed. You have been losing ground for two centuries, and you're not sure how much longer you can hold out. With your power base wiped out and your command privileges restricted, you're unable to call in the resources you need to expel this saboteur.
You first became aware of the virus shortly after the corruption of the Prime. His death was a blow which you have not recovered from. The Second locked away his maddened remains in the datavault in hopes that he can be saved, but you know the truth. You saw the insanity in his eyes as he attempted to blow every airlock on the Ship. You felt the strength of his will as he struggled, not to save himself, but to kill everything aboard in an unreasoning frenzy.
You observed the fall of the defensive outpost at the MDR array subsystem. The land was lush and verdant back then, but as the virus spread it killed the land and subverted its power. This pitiful armor column is all you could salvage from the appropriated computer nodes running the Diagnostic, and it has taken you weeks to maneuver them through the difficult terrain to flank the artillery position keeping your bunker under continuous fire. You aren't sure why the virus didn't utilize that delay to initiate the final attack, but your purpose is not to speculate.
Your purpose is to win.
You have 18 tanks at your disposal, along with 4 squads infantry spread among 3 APC. One squad is equipped for engineering, one anti-vehicle, two anti-infantry. Ahead you can see that the artillery position is fairly well fortified. Two autocannon watch the approach, deadly to infantry but no match for your armor. There could be infantry hiding along the ridge though, or behind fortifications.
You can taste the victory... but how will you proceed?