What is the explanation of Master Chief receiving the gifts from the Librarian if she is dead?
Again, in Spartan Ops Halsey gets to the Librarian. Where is she, and if she's dead how is this happening?
Promethean Knights were composed humans, but what are the Crawlers and Watchers? Their dogs and birds?
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Librarian left an imprint of herself on Requiem before she stranded herself on Earth. She had intended for the Ur-Didact's mind to be healed by the Domain so he could awaken to be the steward of humanity's ascension to the Mantle. Watchers are composed children, we don't know what Crawlers are though.