Database

db={"stores":[{"_id":1,"item":"test store"}],"services":[{"_id":1,"store":1,"description":"service 1","categories":[1,3]},{"_id":2,"store":1,"description":"service 2","categories":[2]}],"categories":[{"_id":1,"name":"cat 1"},{"_id":2,"name":"cat 2"},{"_id":3,"name":"cat 3"}]}

Query

db.stores.aggregate([{"$lookup":{"from":"services","localField":"_id","foreignField":"store","as":"services"}}])

Result