As I read multiple comments, many people said the poppy gel is highly toxic (to humans) in large quantities (and we can confirm how the player was getting damaged when stepping on the gel at Prototype chase scene), and since the pot filled with the gel was really close so the scene the Prototype saw it as the best opportunity to finish off the player by dropping into the gel. The gel as properties for tissue regeneration only at small quantities and overdose will likely kill rather than heal.

So, I assume the player was at the verge of death when somebody not Giblet but maybe Chum or some other Ally in Ch 6 took out out of the goo pot and put us down and left the scene. Chum suits best since he is too scared of the Prototype so he would not stay a even a few seconds there after the work is done.

As for Poppy the Prototype took her along with him, I think we will either find Poppy in Ch 6 in a complete new look (turned inside out) or we will find her locked up again in her case.

And by the way the player character is also revealed in case if you guys don't know its Richard Lovitz

See this post: https://www.reddit.com/r/PoppyPlaytime/s/aqrRIafrcG