Database

db={"distributors":[{"uid":"d1","name":"Distributor 1",/** more attributes here*/"children":[{"name":"Country 1",/** more attributes here*/"children":[{"name":"City 1",/** more attributes here*/"children":[{"name":"Shop 1",/** more attributes here*/"children":[{"name":"Fruit 1",/** more attributes here*/"child":"f1"}]}]}]}]}],"fruits":[{"uid":"f1","name":"Fruit 1 Detail","variants":[{"uid":"v1","name":"Variant 1","tools":["t1","t2"]},{"uid":"v2","name":"Variant 2","tools":["t3","t4"]}]},{"uid":"f2","name":"Fruit 2 Detail","variants":[{"uid":"v1","name":"Variant 1","tools":["t1","t2"]},{"uid":"v2","name":"Variant 2","tools":["t3","t4"]}]}],"tools":[{"uid":"t1","name":"Tool 1"},{"uid":"t2","name":"Tool 2"},{"uid":"t3","name":"Tool 3"},{"uid":"t4","name":"Tool 4"}]}

Query

db.distributors.aggregate([{"$match":{"uid":"d1"}},{$lookup:{from:"fruits",localField:"children.children.children.children.child",foreignField:"uid",as:"fruits"}},{$lookup:{from:"tools",localField:"fruits.variants.tools",foreignField:"uid",as:"tools"}},{$set:{tools:"$$REMOVE",fruits:{$map:{input:"$fruits",as:"f",in:{$mergeObjects:["$$f",{variants:{$map:{input:"$$f.variants",as:"v",in:{$mergeObjects:["$$v",{tools:{$map:{input:"$$v.tools",as:"t",in:{$arrayElemAt:["$tools",{$indexOfArray:["$tools.uid","$$t"]}]}}}}]}}}}]}}}}},{$project:{countriesA:{$map:{input:"$children",as:"country",in:{$mergeObjects:["$$country",{children:{$map:{input:"$$country.children",as:"city",in:{$mergeObjects:["$$city",{children:{$map:{input:"$$city.children",as:"shop",in:{$mergeObjects:["$$shop",{children:{$map:{input:"$$shop.children",as:"fruit",in:{$mergeObjects:["$$fruit",{child:{$arrayElemAt:["$fruits",{$indexOfArray:["$fruits.uid","$$fruit.child"]}]}}]}}}}]}}}}]}}}}]}}}}}])

Result