So basically this is a bug that has (appareantly) been in D2 since june (last report i saw was in june 2019) and has been effecting a decent amount of the player base. So basically if you slot a rune before the quest tells you to, your chalice effectively becomes softlocked and you can't unlock menagerie anymore. Basically this is how the bug happens: First you get the chalice and the chalice slot already unlocked before even obtaining the imperials (somehow this happened to me) and then you slot a rune before the quest tells you to. This basically softlocks the chalice as when the game gives you a rune to slot in your chalice you can't and you can't remove the already existing rune from your chalice effectively locking the chalice out. The game won't allow you to do menagerie until you slot the rune and you can't insert the rune because you have a rune in the chalice. Please fix this ASAP bungie, thanks.
Link to the video that shows my exact problem:
https://youtu.be/6lmm4uWo0Y4
Kind regards
~me :p
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Try deleting the Leviathan Raid quest... i did this and my chalice quest item opened up for me to slot my rune!