4th Singularity London: Southwark free quest is the best AP & time-saving location to farm Homunculus Baby. You'll get about 3x Homunculus Baby by spending 190AP. Evil Bone is also dropped.
Here is a list of servants that need Homunculus Baby to perform Ascension and Skill Up.
Rashoumon event (Ibaraki Douji event)
Murder at the Kogetsukan
Inheritance of Glory
How to farm EXP cards & level fast
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Altria Pendragon (Lancer Alter)