Database
db={"employees":[{"_id":1,shift:[{id:1,day:"Mon",status:true,shift:[{startTime:"08:00 am",endTime:"09:00 pm"},{startTime:"9:00 am",endTime:"10:00 pm"},{startTime:"10:00 am",endTime:"11:00 pm"},{startTime:"11:00 am",endTime:"12:00 pm"},{startTime:"12:00 pm",endTime:"01:00 pm"},{startTime:"02:00 pm",endTime:"03:00 pm"},{startTime:"03:00 pm",endTime:"04:00 pm"},{startTime:"04:00 pm",endTime:"05:00 pm"}]},{id:2,day:"Tue",status:true,shift:[{startTime:"08:00 am",endTime:"09:00 pm"},{startTime:"9:00 am",endTime:"10:00 pm"},{startTime:"10:00 am",endTime:"11:00 pm"},{startTime:"11:00 am",endTime:"12:00 pm"},{startTime:"12:00 pm",endTime:"01:00 pm"},{startTime:"02:00 pm",endTime:"03:00 pm"},{startTime:"03:00 pm",endTime:"04:00 pm"},{startTime:"04:00 pm",endTime:"05:00 pm"}]},{id:3,day:"Wed",status:true,},{id:4,day:"Thu",status:true,shift:[{startTime:"08:00 am",endTime:"09:00 pm"},{startTime:"9:00 am",endTime:"10:00 pm"},{startTime:"10:00 am",endTime:"11:00 pm"},{startTime:"11:00 am",endTime:"12:00 pm"},{startTime:"12:00 pm",endTime:"01:00 pm"},{startTime:"02:00 pm",endTime:"03:00 pm"},{startTime:"03:00 pm",endTime:"04:00 pm"},{startTime:"04:00 pm",endTime:"05:00 pm"}]},{id:5,day:"Fri",status:true,shift:[{startTime:"08:00 am",endTime:"09:00 pm"},{startTime:"9:00 am",endTime:"10:00 pm"},{startTime:"10:00 am",endTime:"11:00 pm"},{startTime:"11:00 am",endTime:"12:00 pm"},{startTime:"12:00 pm",endTime:"01:00 pm"},{startTime:"02:00 pm",endTime:"03:00 pm"},{startTime:"03:00 pm",endTime:"04:00 pm"},{startTime:"04:00 pm",endTime:"05:00 pm"}]},{id:6,day:"Sat",status:false,shift:[],},{id:7,day:"Sun",status:false,shift:[],},]}],"bookings":[{"_id":1,"employee_id":1,"day_id":2,"slot":3},{"_id":2,"employee_id":1,"day_id":5,"slot":4}]}
Query
db.employees.aggregate([{"$unwind":{path:"$shift"}},{"$unwind":{path:"$shift.shift",includeArrayIndex:"arrayIndex"}},{"$lookup":{from:"bookings",let:{arrayIndex:"$arrayIndex",shift_id:"$shift.id"},pipeline:[{$match:{$expr:{$and:[{$eq:["$$shift_id","$day_id"]},{$eq:["$$arrayIndex","$slot"]}]}}}],as:"bookings"}},{"$match":{"bookings":{"$size":0}}}])