Database
[{_id:"UNIQUE_ID",myarray:[{mykey:"11111"},{nestedarray:[{mykey:"22222"},{mykey:"84325"}]},{mykey:"645644"},{nestedarray:[{mykey:"23242"},{mykey:"23433"}]}]}]
Query
db.collection.aggregate([{$project:{myarray:{$filter:{input:"$myarray",cond:{$or:[{$in:["$$this.mykey",["11111","22222"]]},{$anyElementTrue:[{$map:{input:{$ifNull:["$$this.nestedarray",[]]},as:"na",in:{$in:["$$na.mykey",["11111","22222"]]}}}]}]}}}}}])