the puppets represent
the scientist's emotional state when that part of his soul was transferred into the talisman. i imagine doing that was a very laborious process, spanning days maybe even weeks, and as he went forth with his project, he went through many different phases of the mind.
1- anger at what had happened to the world, stubbornness toward a single goal
2- the willingness to press forward
3 and 4- the need to hold on, to preserve whatever is left
5- fear, uncertainty
6- scientific delirium
7- bravery, determination
8- resolution, mixed with the numbing sensation of being totally spent
9- final renewed sense of purpose, clarity, being at peace
at least, these are what i gathered in one passing of the movie..
Oh no! I misspelled one word and suddenly my entire argument is dismantled.