Database

db={"Tours":[{"_id":ObjectId("5f3122f4d8d57e3b9650e5b4"),"title":"tour 1","locations":[{"destination":{"id":ObjectId("5ec5ae9037ea99f20a79071a")},"services":{"hotel":true}},{"destination":{"id":ObjectId("5ec5ae8e37ea99f20a78ef8c")},"services":{"hotel":true}}]},{"_id":ObjectId("5f2d65e68bc6e9155310d147"),"title":"tour 2","locations":[{"destination":{"id":ObjectId("5ecf994435c3a6025d5bf126")},"services":{"hotel":true}}]},{"_id":ObjectId("5f2d66398bc6e9155310d161"),"title":"tour 3","locations":[{"destination":{"id":ObjectId("5ec5ae8e37ea99f20a78ef8d")},"services":{"hotel":true}}]},],"Destinations":[{"_id":ObjectId("5ec5ae9037ea99f20a79071a"),"name":"dest 1","country":"country name"},{"_id":ObjectId("5ec5ae8e37ea99f20a78ef8c"),"name":"dest 2","country":"country name"},{"_id":ObjectId("5ec5ae8e37ea99f20a78ef8d"),"name":"dest 3","country":"country name"},{"_id":ObjectId("5ecf994435c3a6025d5bf126"),"name":"dest 4","country":"country name"}]}

Query

db.Tours.aggregate([{"$unwind":"$locations"},{$lookup:{from:"Destinations",localField:"locations.destination.id",foreignField:"_id",as:"destination"}},{"$project":{"title":"$title","locations":{"destination":{"$arrayElemAt":["$destination",0]},"services":"$locations.services"}}},{"$group":{"_id":"$_id","title":{"$first":"$title"},"locations":{$push:"$locations"}}}])

Result