Database

db={"settings":[{"_id":ObjectId("5e93fea52f804ab99b12e7c0"),"section":"section-1","terminal":"terminal-1","isActive":true,"isDelete":false,"type":"This is section-1 terminal-1 first config."},{"_id":ObjectId("5e93fea52f804ab99b12e7c1"),"section":"section-1","terminal":"terminal-1","isActive":true,"isDelete":false,"type":"This is section-1 terminal-1 second config."},{"_id":ObjectId("5e93fea52f804ab99b12e7c2"),"section":"section-1","terminal":"terminal-2","isActive":true,"isDelete":true,"type":"This is section-1 terminal-2 first config."},{"_id":ObjectId("5e93fea52f804ab99b12e7c3"),"section":"section-2","terminal":"terminal-1","isActive":true,"isDelete":true,"type":"This is section-2 terminal-1 first config."},]}

Query

db.settings.aggregate([{$group:{_id:{section:"$section",terminal:"$terminal"},v:{$addToSet:{_id:"$_id",isActive:"$isActive",isDelete:"$isDelete"}}}},{$group:{_id:"$_id.section",v:{$push:{k:"$_id.terminal",v:"$v"}}}},{$replaceRoot:{newRoot:{$arrayToObject:[[{k:"$_id",v:{$arrayToObject:"$v"}}]]}}}])

Result