Database

db={"Profile":[{"_id":ObjectId("5ec62ccb8897af3841a46d46"),"u":"Test User","is_del":false}],"Store":[{"_id":ObjectId("5eaa939aa709c30ff4703ffd"),"id":"5ec62ccb8897af3841a46d46","a":{"ci":"Test City","st":"Test State"},"ip":false,"op":[],"b":["normal"],"is_del":false}],Item:[{"_id":ObjectId("5ea98a25f1246b53a46b9e10"),"sid":"5eaa939aa709c30ff4703ffd","n":"sample","is_del":false}]}

Query

db.Profile.aggregate([{$match:{is_del:false}},{$lookup:{from:"Store",as:"stores",let:{pid:{$toString:"$_id"}},pipeline:[{$match:{is_del:false,$expr:{$eq:["$$pid","$id"]}}},{$lookup:{from:"Item",as:"items",let:{sid:{$toString:"$_id"}},pipeline:[{$match:{is_del:false,$expr:{$eq:["$$sid","$sid"]}}},{$count:"count"}]}},{$unwind:"$items"}]}}])

Result