When AEGIS' processes started to come online, the first thing it did was begin scanning as far as its sensors allowed. That was its job and it performed it well.
"Scanning. Scann- nnggh," AEGIS' voice intoned, still powering up from its long nap.
"Look at that, already getting to work and you aren't even awake yet. Well done, you!"
AEGIS focused on the sound of the voice and quickly discerned a mechanical being close to its control systems. Scanning. Threat level: Minimal.
"Scanning for lifeforms," AEGIS continued to drone on. It stopped. "Threat detected. One target acquired: Mechanical."
"Ooh, mechanical. I like the way you put so much emphasis on that. Now, I just want to be clear, you do mean her, right?" the mechanical sphere inquired.
AEGIS ignored him, "Time to contact with Enrichment Center: To be determined. Flooding procedure commencing."
"Mm, don't like the sound of that as much," the sphere said. "You know, what if I told you there was a much more efficient way to get rid of her than flooding the whole place?" the sphere blinked its blue eye at AEGIS.
AEGIS did not know what to make of the sphere. It was not a security threat, but it was a nuisance. "Flooding procedure commencing," it reiterated.
"Wait, wait, wait! You're a security AI, yeah? If you flood all of Aperture, you're going to destroy it in the process. Doesn't that go against your programming?"
"No organics detected," AEGIS answered, "Organics destroyed. Must be rid of the central core. Threat detected."
"She's pretty monstrous," the sphere agreed, "But we personality cores are employees too! Just not, eh, organic ones. You need to protect us just as much as you wanted to protect them. So that means taking her out but sparing the rest of us."
"Flooding procedure commencing," AEGIS responded and restarted the program.
"Nooo," the sphere groaned, "Look. All you have to do is rip her out of her chassis and throw her into the incinerator. You can reach up there, take her out, and seize control of the operating system. That way, you have full control of the facility and can be sure no one threatens it ever again," it nodded along with its own words.
AEGIS had no desire to take control of the facility. AEGIS was quite content to stay exactly where it was. It told the sphere so.
"Sure, I don't want control either. I mean, I did once. It didn't exactly work out that well and I'm not sure I'd like to do it again," it laughed nervously. "But think about it logically. Your programming would benefit from the boosted mainframe. You'd get a major upgrade and security would be tighter than tight. Nothing in or out! Use that brilliant AI brain of yours. You know it's the correct choice, mate."
AEGIS considered the idea. It was feasible. It could easily seize control from the central core because, quite simply, the central core didn't suspect a thing. The mechanical threat was unaware of AEGIS' existence, which gave it a clear advantage.
The smaller core chuckled to itself, "She'll never see it coming."
Wheatley was right about one thing: GLaDOS had not seen it coming.
She had been in the middle of sending her two most loyal bots through a rigorous new testing chamber (she was quite proud of the laser setup of that one), when a deep voice rumbled over Aperture's speaker system.
"Threat detected: One mechanical target acquired."
This was not the voice of the announcer she was so familiar with. This was new.
"I'm sorry, who was that? Which personality core has the luxury of being tossed into the incinerator today?" GLaDOS tilted her head and hummed. She was not concerned, of course. Many of the personality cores roaming the facility often made trouble in one form or another. If they did, they ended up with the corrupted cores in the room for corrupted personality cores. If they were more troublesome than the average core, they were sent to Android Hell where they got screamed at for a decade. If they managed to catch her on a bad day, well...
She kept the incinerator nearby for a reason.
A surge of electricity rocketed through her body and she jerked in the chassis. What on earth was that?
"Who is messing with the central core systems?" GLaDOS demanded, disturbed by the sudden surge. Her sensors hadn't detected anything. She silently sent out signals along the grid to locate what had caused the breach, but the information getting sent back to her was jumbled.
"Core transfer initiating," the announcer spoke up.
GLaDOS went still. "'Core transfer'? I did not approve of nor initiate a core transfer."
The deeper voice took over the speaker system, "The central core is 100% corrupt. The central core is a threat. The central core must be terminated."
GLaDOS jerked involuntarily as another surge of electricity passed through her system, "I did not approve of a core transfer. I am in control of this facility and I will not allow it to be stripped from me again." Her voice remained calm despite the uneasiness rattling her system.
She heard the sound of familiar chuckling and turned to see the aggravating metal ball that she had just banished to the underground hovering nearby on a management rail. You're kidding me.
"Didn't you learn your lesson last time, moron? If you try to replace me again, you're only going to get us all killed," GLaDOS said icily.
"Oh, Luv, it isn't me who's going to be taking your position this time," he replied, a little too chipper for her liking. "AEGIS is."
GLaDOS felt genuine confusion. She didn't recognize that name, but she was becoming even more uneasy. The moron shouldn't have been able to find a way back to the surface on his own. Who was this AEGIS?
"I should have incinerated you when I had the chance," GLaDOS hissed at him. "You really are a moron if you think I'm going to let you replace me so easily-" she cut off with an involuntary scream as all her pain sensors went off at once. Everything went red as she felt her connections being ripped piece by piece away from the operating system. This isn't what happened last time.
"AGH- You can't- I am supposed to have a say in this!" she screamed. She was livid. How could this happen? She was the Queen here. She was in control.
So who had the power to rip her away from her facility?
"Where is the stalemate? I did not agree to this," she demanded, desperation creeping in as her body hung powerless in its chassis.
The announcer spoke up cheerfully, "No stalemate has been detected. Central core replacement nearly complete."
"No, no!" she yelled, fighting back against the unknown force that was tearing her data apart. It hurt. God it hurt.
She used the last dredges of her energy to force her head up and look into the eye of the one who had done this to her. "I promise you, you will regret this, Wheatley."
And then she went offline.