SPOILER ALERT!

At the end of Portal you face the final boss, really the only boss.  Her name is GLaDOS.  GLaDOS stands for Genetic Lifeform and Disk Operating System.  Throughout the game she slowly becomes more and more emotional.  At the beginning she sounds just like any AI, but by the end of the game she is angry and haughty and he voice hides none of it.  As she talks to you something falls out of her.  After the Morality core is thrown in the Aperture Science Emergency Intelligence Incinerator, GLaDOS changes.   That is when you learn more about the past of the Aperture Science Center.  She releases a deadly neurotoxin into the chamber.

“When I said "deadly neurotoxin," the "deadly" was in massive sarcasm quotes. I could take a bath in this stuff. Put it on cereal, rub it right into my eyes. Honestly, it's not deadly at all … to me. You, on the other hand, are going to find its deadliness a lot less funny.” -GLaDOS

You have three minutes to throw the rest of GLaDOS’s cores into the incinerator or you will die of gas poisoning.  Should you succeeded GLaDOS begins getting torn apart and as she flies out of the building you get pulled out with her.  The next thing the screen shows you is GLaDOS scattered all around you.  You are unable to move, you are assumed dead.  The Credits begin to roll and GLaDOS begins to sing.

When the decision came that Portal 2 was being released the ending changed ever so slightly.

This is my favorite quote that GLaDOS says during the battle.