You could use a Set for this, together with a recursive function to flatten the result, and then finally apply a basic sort on it:

function getValues(arr) {
  return [...arr.reduce( (acc, val) => 
    new Set([...acc, ...(Array.isArray(val) ? getValues(val) : [val])]), [])];
}
// Sample input
var array_input = [2,1, [1,3,2], [4,5,6, [9,8,10]]];
// Get values and sort them
var result = getValues(array_input).sort( (a,b) => a-b );
// Show output
console.log(result);

Object keys alternative

The same principle can be used with an object using the values as keys, although I prefer the Set way. As object keys are iterated in numerical order (when they are numerical), the explicit sorting step is not needed here:

function getValuesAsKeys(arr) {
  return arr.reduce( (acc, val) => 
    Object.assign(acc, Array.isArray(val) ? getValuesAsKeys(val) : { [val]: val }), {} );
}

// Sample input
var array_input = [2,1, [1,3,2], [4,5,6, [9,8,10]]];
// Get values and sort them
var result = Object.values(getValuesAsKeys(array_input));
// Show output
console.log(result);

NB: The Object.values method has at this moment little support. Object.keys(getValues(array_input)).map(Number) can be used instead as in this object the keys are the values, but in string type (of course).

Number-String-Number alternative

Converting the array to string is another possibility, but I don't really like to perform conversion when in the end you need the numbers, not strings.

Ok I am using a bunch of things form different sources. First to condense the array, @Thalaivar's answer nails it.

var array_input = [1,2, [1,2,3], [4,5,6, [9,8,10]]];
var pArray = array_input.join().split(',').map(Number);

Then, using this answer ad some slight modification (implement a number sort), we will remove any duplicates form the array while sorting it:

function uniqSort(a) {
    return a.sort(function sortNumber(a,b) {
        return a - b;
    }).filter(function(item, pos, ary) {
        return !pos || item != ary[pos - 1];
    })
}

Then just call that function.

var array_output = uniqSort(pArray);

var array_input = [1,2, [1,2,3], [4,5,6, [9,8,10]]];
console.log(array_input.join().split(',').map(Number));

You could use the above... https://jsfiddle.net/vp9kq3a8/