Kindergarten

Lily's quest is the final quest in the game, completing it will result in beating the game, aside from the Talismans ending.

Required Items Edit
Office Key
Teacher's Phone
Billy's Note
$3.00

Home/Schoolyard
Talk to Lily, show her the note, she will freak out and ask you to find someone that can read it.
Talk to Monty, he will read the note for $1.00. He then says he needs until lunchtime because the handwriting is atrocious.
Talk to Monty once more, buy the cigarettes.
Talk to Lily, let her know, then show her the phone and key as prompted.
Talk to Nugget about Billy until sent to the principal's office.
Tell the Principal that you're sad and get the pills. Then interact with the rug (located at the bottom-right corner of room), lift it, and the secret hatch will be revealed.

Morning Time
Talk to Lily
Go to the exit, ask Ms. Applegate for the bathroom pass, then go to the restroom.
Check all the stalls, talk to The Janitor, and get him to clean the last stall. Grab the finger from the box he was standing near (far right on the bottom) or Billy's shoe from the box furthest to the left.
Return to class, triggering lunchtime.

Lunchtime
Talk to Monty, get the code
Talk to Lily, she's already payed the Lunch Lady. Follow her into the hall, then into the bathroom.
The Hall Monitor will be in the bathroom. Give him the Cigarettes you bought from Monty at the school yard.
Give Lily the phone, she's going to call the Principal to get him out of his office. Follow her to the entrance to the principal's office, then unlock it and go inside. Lily informs that the trap uses a key, not a code. Go behind the left side of the principal's desk, a red exclamation point will appear, then use the code on the desk and get the hatch key. Use the key on the trapdoor.

The Principal's Lab
The computer controls are as follows:

Yellow: Switch tanks
Red: Kill test subject
Green: Revert mutation
Blue: Release all viable test subjects.
The order the buttons need to be pressed to successfully complete the mission:

Yellow, to switch to the first tank containing a creature.
Red, to kill the creature in the first tank. Failure to do this will result in the creature killing you.
Yellow, to switch to the 2nd tank (Billy's tank).
Green, to revert the mutation process on Billy. This action does not work on the other two tanks.
Blue, to release contents of all viable tanks. If you fail to revert the mutation process on Billy, he will not be released upon pressing the blue button. If this happens but you manage to kill the Principal with the other creature, the computer will destroy any evidence of the principal's experiments by killing/blending Billy.
Before you can do step #5, the Principal will show up and confront you and Lily. The Principal will then explain the meaning behind all his experiments, before saying he's going to kill you. Once the Principal is finished talking, you will have the chance to perform step #5. If done correctly, Billy will then be released from his tank, and The Principal will get killed by one of the creatures.