[{"value":{"shipmentId":1079,"customer_orders":[{"customer_order_id":1124,"active":false},{"customer_order_id":1277,"active":true,"items":[{"item_id":281,"active":false,"qty":1,"name":"apples","attributes":null},{"item_id":282,"active":true,"qty":2,"name":"bananas"}]}],"carrier_orders":[{"carrier_order_id":744,"active":true}]}}]

db.collection.aggregate([{"$match":{"value.shipmentId":{"$in":[1079]}}},{"$project":{"value.shipmentId":1,"value.customer_orders":1,"value.carrier_orders":1,}},{"$addFields":{"value.customer_orders":{$filter:{input:"$value.customer_orders",as:"customer_order",cond:{$eq:["$$customer_order.active",true]}}},"value.carrier_orders":{$filter:{input:"$value.carrier_orders",as:"carrier_order",cond:{$eq:["$$carrier_order.active",true]}}}}},{$set:{"value.customer_orders":{$map:{input:"$value.customer_orders",in:{$mergeObjects:["$$this",{items:{$filter:{input:"$$this.items",as:"item",cond:{$eq:["$$item.active",true]}}}}]}}}}}])