[{"domain":"foo.com","altNames":[]},{"domain":"bar.com","altNames":[]},{"domain":"zaz.com","altNames":["foo.com","bar.com"]},{"domain":"baz.com","altNames":["boo.com"]}]

db.collection.aggregate([{"$lookup":{"from":"collection",let:{d:"$domain"},pipeline:[{"$match":{$expr:{$in:["$$d","$altNames"]}}},{$limit:1}],"as":"altNamesLookup"}},{"$match":{altNamesLookup:[]}},{"$project":{altNamesLookup:false}}])