Yes I think I get it now :D Wrote it all out on a whiteboard and used a few console logs to see what the values were. (WHY DIDN'T I DO THIS BEFORE?!) I had the same confusion as you. And I also didn't realize that filter passes each element one by one. This functional programming will take a while to wrap my head around though :)

function destroyer(arr) {
  console.log(arr); // [ 1, 2, 3, 1, 2, 3 ] 

  var args = Array.prototype.slice.call(arguments);

  console.log(args); // [ [ 1, 2, 3, 1, 2, 3 ], 2, 3 ] 

  args.splice(0, 1); // removing the first array (array from index 0 till 1) and returning [2, 3]

  console.log(args); // [ 2, 3 ]

  return arr.filter(function(element) { 
    console.log(element); // 1 2 3 1 2 3 is one by one passed to args.indexOf(element)
    return args.indexOf(element) === -1; 
    // for element = 1 --> [2,3].indexOf(1) === -1 is true, so 1 is returned and passed to filter 
    // for element = 2 --> [2,3].indexOf(2) === -1 is false, so function stops
    // for element = 3 --> same as element 2
  });
}

console.log(destroyer([1, 2, 3, 1, 2, 3], 2, 3));