Database
db={inspection:[{"_id":{"$oid":"635c37d00017b0adec605f01"},"REF_InspectionItems":[{"$oid":"635c37d30017b0adec605f1d"},{"$oid":"635c37d60017b0adec605f34"}]}],inspectionitems:[{"_id":{"$oid":"635c37d30017b0adec605f1d"},"name":"Water","REF_InspectionItemNotes":[{"$oid":"635c37d40017b0adec605f26"},{"$oid":"635c37d50017b0adec605f2c"}]},{"_id":{"$oid":"635c37d60017b0adec605f34"},"name":"Fire","REF_InspectionItemNotes":[{"$oid":"635c37d70017b0adec605f3d"}]}],inspectionitemnotes:[{"_id":{"$oid":"635c37d40017b0adec605f26"},"text":"Water note 1"},{"_id":{"$oid":"635c37d50017b0adec605f2c"},"text":"Water note 2"},{"_id":{"$oid":"635c37d70017b0adec605f3d"},"text":"Fire note 1"}]}
Query
db.inspection.aggregate([{"$lookup":{"from":"inspectionitems","localField":"REF_InspectionItems","foreignField":"_id","as":"inspectionItemsLookup"}},{"$lookup":{"from":"inspectionitemnotes","localField":"inspectionItemsLookup.REF_InspectionItemNotes","foreignField":"_id","as":"inspectionItemNotesLookup"}},{$set:{items:{$map:{input:"$inspectionItemsLookup",as:"item",in:{$mergeObjects:["$$item",{notes:{$filter:{input:"$inspectionItemNotesLookup",cond:{$in:["$$this._id","$$item.REF_InspectionItemNotes"]}}}}]}}}}},{$unset:["REF_InspectionItems","inspectionItemsLookup","inspectionItemNotesLookup","itemNotes"]}])