Database

db={"courses":[{"_id":ObjectId("5f6a6b159de1304fb885b194"),"title":"Course test","sections":[{"_id":ObjectId("5f6a6b159de1304fb885b195"),"title":"Section 1 - introduction","order":1,"modules":[{"_id":ObjectId("5f6a6b159de1304fb885b196"),"module_FK_id":ObjectId("5f6a6b149de1304fb885b135"),"title":"Module 1","order":1},{"_id":ObjectId("5f6a6b159de1304fb885b198"),"module_FK_id":ObjectId("5f6a6b149de1304fb885b14a"),"title":"Module 2","order":2},]},{"_id":ObjectId("5f6a6b149de1304fb885b175"),"title":"Section 2 - How to do something","order":2,"modules":[{"_id":ObjectId("5f6a6b149de1304fb885b141"),"module_FK_id":ObjectId("5f6a6b149de1304fb885b150"),"title":"Module 1","order":1},{"_id":ObjectId("5f6a6b149de1304fb885b15f"),"module_FK_id":ObjectId("5f6a6b149de1304fb885b18e"),"title":"Module 2","order":2},]},]}],"modules":[{"_id":ObjectId("5f6a6b149de1304fb885b135"),"text":"Lorem ipsum...","mediaUrl":"urllinkhere"}]}

Query

db.courses.aggregate([{$unwind:"$sections"},{$unwind:"$sections.modules"},{"$lookup":{"from":"modules","localField":"sections.modules.module_FK_id","foreignField":"_id","as":"module_details"}},{$unwind:{path:"$module_details",preserveNullAndEmptyArrays:true}},{"$project":{title:1,sections:{_id:"$sections._id",modules:{_id:"$sections.modules._id",module_FK_id:"$sections.modules.module_FK_id",order:"$sections.modules.order",title:"$sections.modules.title",mediaUrl:"$module_details.mediaUrl",text:"$module_details.text"},order:"$sections.order",title:"$sections.title"}}},{"$group":{"_id":"$sections._id",main_id:{$first:"$_id"},main_title:{$first:"$title"},order:{$first:"$sections.order"},title:{$first:"$sections.title"},modules:{$push:"$sections.modules"}}},{"$project":{"_id":"$main_id","title":"$main_title",section:{_id:"$_id",modules:"$modules",title:"$title",order:"$order",}}},{$group:{_id:"$_id",title:{$first:"$title"},sections:{$push:"$section"}}}])

Result