[{"_id":1,"data":[{"id":1,"one":[{"user":2,"two":2},{"user":1,"two":3}]}]},{"_id":2,"data":[{"id":2,"one":[{"user":2,"two":2},{"user":1,"two":3}]}]}]

db.collection.aggregate([{"$project":{"data":{"$filter":{"input":{"$map":{"input":"$data","in":{"id":"$$this.id","one":{"$filter":{"input":"$$this.one","as":"on","cond":{"$eq":["$$on.user","$_id"]}}}}}},"as":"d","cond":{"$eq":["$$d.id","$_id"]}}}}}])