[{"permissions":[{"owners":["1"]}]},{"permissions":[{"owners":["2","3"]}]}]

db.collection.aggregate([{"$unwind":"$permissions"},{"$set":{"owner":{"$in":["2","$permissions.owners"]}}},{"$group":{"_id":"$_id","permissions":{"$push":"$permissions"},"owner":{"$push":"$owner"}}},{"$set":{"owner":{"$in":[true,"$owner"]}}}])