Database

db={users:[{_id:"5ec6d940b98e8f2c3cea5f22",name:"test one",email:"test@example.com"}],skills:[{_id:"5ec786b21cea7d8c8c186a54",title:"java"}],userskills:[{_id:"5ec7879c1cea7d8c8c186a56",skillId:"5ec786b21cea7d8c8c186a54",userId:"5ec6d940b98e8f2c3cea5f22",level:"good"}]}

Query

db.users.aggregate([{$lookup:{from:"userskills",let:{user_id:"$_id"},pipeline:[{$match:{$expr:{$eq:["$$user_id","$userId"]}}},{$lookup:{from:"skills",localField:"skillId",foreignField:"_id",as:"skill"}},{$unwind:"$skill"}],as:"skills"}}])

Result