Database

[{"name":"course1","code":"C1","levels":[{"levelname":"level01","order":1,"modules":[{"modulename":"title module 01","code":"MC1_01","order":1,"title":"module title 01"},{"modulename":"title module 02","code":"MC1_02","order":2,"title":"module title 02"}]},{"levelname":"level02","modules":[{"modulename":"title module 11","code":"MC1_11","order":1,"title":"module title 01"},{"modulename":"title module 12","code":"MC1_12","order":2,"title":"module title 02"}]}]},{"name":"course2","code":"C2","levels":[{"levelname":"level01","order":1,"modules":[{"modulename":"title module 01","code":"MC2_01","order":1,"title":"module title 01"},{"modulename":"title module 02","code":"MC2_02","order":2,"title":"module title 02"}]},{"levelname":"level02","modules":[{"modulename":"title module 10","code":"MC2_10","order":1,"title":"module title 01"},{"modulename":"title module 11","code":"MC2_11","order":2,"title":"module title 02"}]}]}]

Query

db.collection.aggregate([{$match:{"levels.modules.code":"MC1_02"}},{$addFields:{levels:{$filter:{input:{$map:{input:"$levels",in:{$mergeObjects:["$$this",{modules:{$filter:{input:"$$this.modules",cond:{$eq:["$$this.code","MC1_02"]}}}}]}}},cond:{$ne:["$$this.modules",[]]}}}}}])

Result