Expanding on the theory that entries 1-8 were written by Gaster and the others by Alphys.
I think it's safe to say Flowey was an intended vessel for the first DT experiments before Gaster was thrown in his creation.
Alphys continued this and created Flowey.
Fallen down
There had to be two times monsters had 'fallen down' and had been experimented on.
Shyren's sister met her end in the first one with Aaron and Moldbygg.
So who was in the second one? The answer is in the letters you find on Alphys' desk.
Meaning that everyone else who has become amalgamates are from the first DT experiment.
This blows my mind because I originally made it more complicated.
So basically it's this
1. Gaster and Sans are around when Chara falls. Papyrus might be around but he's not directly involved.
2. Chara dies. Gaster tries to extract DT from the human. A human or two dies.
3. Tori goes to the ruins taking Chara with her. Shyren and other monsters fall down.
5. Asgore retrieves them for Gaster. Gaster learns about Chara and takes the future flower that will become Flowey.
6. Four humans fall all dying at some point. Gaster creates the CORE with the intention of annihilating humans.
7. Gaster disappears and Alphys meets Mettaton.
8. Alphys creates Mettaton's body for the king
9. Asgore hires her.
10. More monsters fall down and she experiments on them.
11. Flowey is created at this point after all seven humans have already died.
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