db={"COMMON":[{"_id":1,"idDirectory":11},{"_id":2,"idDirectory":12}],"DIRECTORY":[{"_id":11,"documents":[{"_id":111,"comment":"Комментарий_1"},{"_id":112,"comment":"Комментарий_2"}]},{"_id":12,"documents":[{"_id":113,"comment":"Комментарий_3"}]}],"DOCUMENT":[{"_id":111,"number":"num_1"},{"_id":112,"number":"num_2"},{"_id":113,"number":"num_3"}]}

db.DIRECTORY.aggregate([{"$project":{"a":"$documents"}},{"$lookup":{"from":"DOCUMENT","localField":"a._id","foreignField":"_id","as":"b"}},{"$project":{"x":{"$map":{"input":"$a","as":"c","in":{"$mergeObjects":["$$c",{"$arrayElemAt":["$b",0]}]}}}}},{"$lookup":{"from":"COMMON","localField":"_id","foreignField":"idDirectory","as":"d"}},{"$unwind":"$d"},{"$project":{"_id":"$d._id","documentsResponse":"$x"}}])