Ok, I really don't know why you have to do all that code to do something so simple. Here's what I see.

You have a large global array of enemies:

Code: (javascript) [Select]

var enemies = [];
enemies[0] = new Enemy("enemy1");
enemies[1] = new Enemy("enemy2");
enemies[2] = new Enemy("enemy3");
enemies[3] = new Enemy("enemy4");

Then, in your battle system you say, come across 4 random enemies? We don't need Knuth shuffle for that.

Code: (javascript) [Select]

var team = new EnemyTeam(GetRandom(enemies), GetRandom(enemies), GetRandom(enemies), GetRandom(enemies));

Where GetRandom is simply, this (what Jest had):

Code: (javascript) [Select]

function GetRandom(array) {
    return array[Math.floor(Math.random() * array.length)];
}

The Knuth Shuffle is primarily used to shuffle a sorted list. It's more useful for something like this:

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var enemy_team = [enemies[0], enemies[0], enemies[1], enemies[2]];
RandomizeArray(enemy_team);
var team = new EnemyTeam(enemy_team[0], enemy_team[1], enemy_team[2], enemy_team[3]);

The use is slightly different, and in this case the Knuth shuffle is really not all that needed. I hope that clarifies somethings.

Most things are cleared up, I'm just confused on other stuff now.

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 var team = new EnemyTeam(GetRandom(enemies), GetRandom(enemies), GetRandom(enemies), GetRandom(enemies)); 

I'm not understanding how I can still reference those elements of EnemyTeam individually.
I need to be able to still reference the Enemies individually so that I can use them in the battle system.

Will I be able to use array.length somehow to obtain their index?

I'm using the script like this:

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var enemies = [];  // <---  Enemy Indexes
enemies[0] = 0;
enemies[1] = 52;
enemies[2] = 11;
enemies[3] = 230;

var team[0] = new EnemysTeam(GetRandom(enemies), GetRandom(enemies), GetRandom(enemies), GetRandom(enemies));

function GetRandom(array) { return array[Math.floor(Math.random() * array.length)]; } 

Then in the battle system I'm referencing the enemies like so:

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 team[ET].E1; 

Would it still grab the index, which is now randomized, through the variable E1?
Or is variable E1 now useless?

Basically, E1 is now E1 = GetRandom(enemies);
I'm not sure if the battle system will still retrieve an index from that. Will it?

I'm not understanding how I can still reference those elements of EnemyTeam individually.
I need to be able to still reference the Enemies individually so that I can use them in the battle system.

Oh, that's in GetRandom:

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function GetRandom(array) { return array[Math.floor(Math.random() * array.length)]; }

Notice the [ ] after "array" It might be a lot of stuff packed into that line but it's all a giant indexer:

Code: (javascript) [Select]

function GetRandom(array) {
    var index = Math.floor(Math.random() * array.length)
    return array[index];
}

It will return the random element, so you don't have to do anything weird with the output. It;'ll return say 52 or 11 from the original array. It'll do just that: return a random element.