If I understand you correctly, you want some application approaching directly the MongoDB and that this content then shows up in AEM/Oak and is reachable through its API.
This is not possible, because Oak does not know of the documents you added outside of its control to the MongoDB. Therefor it will never show up in the indexes. If you want to content to be indexed within Oak, you need to insert into the repository by regular means (Oak/Sling APIs).
HTH,
Jörg