I've always seen it as being
#2 . It also makes the most sense.
1. Angier steps into the machine and sits the gun right next to it.
2. Angier is teleported and his duplicate appears inside the machine.
3. His duplicate sees the gun next to the machine, grabs it, and kills the original Angier.
4. The duplicate knows how the machine works and proceeds to kill clone after clone every night, while he's transported to safety.
Of course everything is made to be in question because of Angier himself saying he didn't know if he would be the one on stage or the one in the tank. But the clones always seemed confused like they didn't what was about to happen.