[{_id:"UNIQUE_ID",myarray:[{mykey:"11111",},{nestedarray:[{mykey:"22222",},{mykey:"84325",}]},{mykey:"645644",},{nestedarray:[{mykey:"23242",},{mykey:"23433",}]}]}]

db.collection.aggregate([{"$project":{"myarray":{"$filter":{"input":{"$map":{"input":"$myarray","as":"arrayitem","in":{"mykey":"$$arrayitem.mykey","nestedarray":"$$arrayitem.nestedarray","aaaa":{"$filter":{"input":"$$arrayitem.nestedarray","as":"vv","cond":{"$in":["$$vv.mykey",["11111","22222"]]}}}}}},"as":"ff","cond":{"$or":[{"$in":["$$ff.mykey",["11111","22222"]]},{"$gte":[{"$size":{"$ifNull":["$$ff.aaaa",[]]}},1]}]}}}}},{"$project":{"myarray.aaaa":0}}])