[{_id:ObjectId("123456789123345678912345"),key1:"value1",key2:"value2",key3:[["val1","val2"],["val1","val3"],["val2","val4"]]}]

db.collection.aggregate([{$addFields:{key3:{$reduce:{input:"$key3",initialValue:[],in:{$setUnion:["$$value","$$this"]}}}}}])