[{"_id":0,"matches":[{"name":"match 1","ids":[{"innerName":"1234"},{"innerName":"3"}]}]},{"_id":1,"matches":[{"name":"match 5","ids":[{"innerName":"123"},{"innerName":"1"}]},{"name":"match 5","ids":[{"innerName":"1"},{"innerName":"1234"},]},]}]

db.collection.find({$expr:{$in:["1234",{$reduce:{input:"$matches",initialValue:[],in:{"$concatArrays":["$$value",[{$last:"$$this.ids.innerName"}]]}}}]}})