Good Ending: There are several things you will want to do to get the best ending, whish is the most satisfying and answers the most questions. 

• Save Flint in Dryfield.
• Open the Full Moon Gate and return to Dryfield from the shelter.  Follow Flint to the Water Tower and save Pierce.
• Read Pierce's memo in the Pod Service Gantry.  Immediately call Jodie.
• Get the Teddy Bear by No. 9's motorcycle.
• Get the note from Flint, and give him the Teddy Bear.
• Rescue Pierce in Golem Freezer.
  
• Save the blinded soldier in the shelter.

Regular Ending: It is much the same as the Good Ending, but you don't call Jodie after reading the memo, or rescue Pierce from the Golem Freezer.

Sad Ending: You will get this if you let Flint die, don't return to Dryfield, and don't save Pierce at the Water Tower.  If Flint dies, he can't lead you to Pierce, bring you a note from Mr. Douglas, take Eve's Teddy Bear, or lead the blinded soldier to safety.  If you don't save Pierce at the Water Tower, you won't get his note in the Pod Service Gantry or rescue him in the Golem Freezer.  All you will get from this path are the Chicken Plate armor and a greater involvement between Kyle and Aya.