Code:
console.log("     Nuke, Foot, Cockroach!");
console.log("          By [email protected]");

/*Variables and game setup*/
var played = 0;
var score1 = 0;
var score2 = 0;
var times = Number(prompt("How often do you want to play?"));
if (isNaN(times)) {
    times = 1;
    console.log("\nInvalid input!\nNumber of rounds set to 1!");
} else console.log("\nYou chose to play " + times + " times.");

/*FUNCTION COMPARING CHOICES*/
var compare = function (choice1, choice2) {
    if (choice1 === choice2) {
        console.log("Its a tie. Choose again!");
    } else if (choice1 === "nuke") {
        if (choice2 === "foot") {
            console.log("Nuke blows up foot.");
            console.log("Player 1 wins this round.");
            score1 += 1;
        } else if (choice2 === "cockroach") {
            console.log("cockroach survives nuke.");
            console.log("The computer wins this round.");
            score2 += 1;
        }
    } else if (choice1 === "foot") {
        if (choice2 === "cockroach") {
            console.log("Foot crushes cockroach.");
            console.log("Player 1 wins this round.");
            score1 += 1;
        } else if (choice2 === "nuke") {
            console.log("Nuke blows up foot.");
            console.log("The computer wins this round.");
            score2 += 1;
        }
    } else if (choice1 === "cockroach") {
        if (choice2 === "foot") {
            console.log("Foot crushes cockroach.");
            console.log("The computer wins this round.");
            score2 += 1;
        } else if (choice2 === "nuke") {
            console.log("Cockroach survives nuke.");
            console.log("Player 1 wins this round.");
            score1 += 1;
        }
    }
};
/*END OF FUNCTION*/

do { // repeats game x times, as specified by player
    played += 1;
    console.log("\nRound " + played + "/" + times);
    do { // repeats code as long as game is tied
        do { // repeats code until player enters proper input
            if (userChoice === "rules") {
                console.log("\nRules:\nNuke blows up foot.");
                console.log("Foot crushes cockroach.");
                console.log("Cockroach survives nuke.");
            }
            var userChoice = prompt("Do you choose nuke, foot or cockroach?", "Type <rules> to see the rules.").toLowerCase();
        } while (userChoice != "nuke" && userChoice != "foot" && userChoice != "cockroach");
        var computerChoice = Math.random();
        if (computerChoice < 0.2) {
            computerChoice = "nuke";
        } else if (computerChoice <= 0.4) {
            computerChoice = "foot";
        } else if (computerChoice <= 0.6) {} else {
            computerChoice = "cockroach";
        }

        console.log("\nYour choice: " + userChoice);
        console.log("Computer: " + computerChoice);

        compare(userChoice, computerChoice);
    } while (userChoice === computerChoice);
} while (played <= times - 1); // times minus 1 because its a do-loop

console.log("\nFinal Score: " + score1 + ":" + score2);
if (score1 > score2) {
    console.log("Player 1 is the overall winner!");
} else if (score2 > score1) {
    console.log("The computer is the overall winner!");
} else {
    console.log("It's a tie after all.");
}