Database

[{name:"first",docs:[{a1:["a","b"],a2:["c"]},{a1:["d","e"],a2:["f"]}]},{name:"second",docs:[{a1:[1,2],a2:[3]},{a1:[4,5],a2:[6]}]}]

Query

db.collection.aggregate([{"$unwind":"$docs"},{$project:{name:1,data:{$objectToArray:"$docs"}}},{$project:{name:1,data:{$reduce:{input:"$data",initialValue:[],in:{$concatArrays:["$$this.v","$$value"]}}}}},{$group:{_id:"$_id",name:{$first:"$name"},docs:{$push:{merged:"$data"}}}}])

Result