I've thought of the whole fight scene and encounter thingy for MagneDOS:
After battling many Team Quantum members, you finally make it to the center of the Aperture Science laboratories, or at least, what is left of it. Unfortunately, you are too late. The Team Quantum admins and their leader Sigmas have already beaten you to the core, and have fitted the personality magnemites onto MagneDOS, because to activate it, you need all 4. The dialogue plays out like this:
Team Quantum grunt: Lord Sigmas, everything is ready. The personality magnemites have been fitted onto MagneDOS. Shall we activate it?
Sigmas: Yes. Tell the people in the control room to activate MagneDOS.
Sigmas realizes that you are in the room as well, and turns toward you
Sigmas: Oh, looks like you managed to get through. Well, if you were focusing on your survival, that's too bad. Why? Because when we activate MagneDOS, we are gonna use it to slaughter all that stand in our way, starting with YOU!!!
A rumbling noise is heard coming from the AI, and it starts to light up
Sigmas: Yes! YES!!! Its ACTIVATING!!!
The rumbling gets louder and louder, until the entire room starts shaking. Then, the rumbling stops, and with the remaining lights coming on, MagneDOS rises to greet those that are around her.
MagneDOS: Hello..hellool...gelelohello...andwelcometothe Aperture Science computer aided enrichment center.
Admin Buric: It works...MagneDOS is alive!
MagneDOS: Of course I am.
Admin Renia: Hey, it seems to be aware of it's environment.
Admin Niko: To me, it looks like a triumph!
The admins and grunts celebrate their success, while MagneDOS turns her attention to the game's music
MagneDOS: What is this sound playing on the Aperture Science Dedicated Radio Channel? It is interesting, but it is not needed to do what I must do.
Admin Renia: What do you mean?
Admin Niko: What is it that you need to do?
MagneDOS: I must do, what I can do.
Admin Buric: What is she saying Sigmas? What CAN she do exactly?
MagneDOS: Well, since I am linked with every system in this complex, basically anything.
The music then changes from pokemonish music to this
http://www.youtube.com/watch?v=cjgaDYzdmiI which btw will loop once it gets to 24 seconds back to the first second until you start battling her, in which it then starts at the 25 second mark and loops back there when it gets to the end
MagneDOS: Ah, I think I found a more suitable sound for the upcoming situation. This was a triumph. We are out of alpha. Now it's hard to overstate my satisfaction. But I've experiments to run. There is research to be done. Now, goodbye!
Admin Niko: Everyone get the hell out of here!
The Team Quantum members quickly head for the exit, much to MagneDOS's annoyance
MagneDOS: That has got to be the dumbest thing that-whoa WHOA whooaaa...hehehehehe...
With her conscious and morality forgotten, MagneDOS begins firing death lasers and flinging Team Quantum members around with telekinesis. After a few moments, a bunch of Team Quantum members are lying there dead. THEN she turns her attention to YOU.
MagneDOS: You...you are interesting. You don't seem to be very afraid. After all that, you won't back down. Very well then, I'll have to deal with you personally. You may not be afraid now, but trust me, I will have you begging me not to end your pitiful and evil life in moments. And by the way, I won't listen to your begging. Because the only thing you deserve...is to DIE!!!
MagneDOS then engages you into battle. Details coming soon!