1. int timerLength = 60000; // 60 seconds
2. int currentLevel, endTime;
3. boolean timerOn;
4.  
5. void setup() {
6.   size(500, 500);
7.   textSize(40);
8.   textAlign(LEFT, TOP);
9. }
10.  
11. void draw() {
12.   background(0);
13.   text("(press space)", 10, 10);
14.   text("currentLevel: " + currentLevel, 10, 110);
15.   if (timerOn) {
16.     int remainingTime = endTime-millis();
17.     if (remainingTime <= 0) {
18.       println("The End!");
19.       timerOn = false;
20.     } else {
21.       text("countdown: " + remainingTime/1000, 10, 210);
22.     }
23.   }
24. }
25.  
26. void keyPressed() {
27.   if (key == ' ') {
28.     currentLevel++;
29.     if (currentLevel == 3) {
30.       endTime = millis() + timerLength;
31.       timerOn = true;
32.     }
33.   }
34. }

1. Car[] cars = new Car[10];
   int[] lanes = {
     135, 235, 335, 435
   };
   int[] carSpeeds = {
     -12, 8, -6, 4
   };
   int[] pirateSpeeds = {
     -8, -6, -4, -2, 2, 4, 6, 8
   };
   
   
   Fuel[] cells = new Fuel[20];
   
   Pirate[] pirates = new Pirate[6];
   
   
   PImage img;
   PImage imgCar;
   PImage imgSplash1;
   PImage imgSplash2;
   PImage imgSplash3;
   PFont f;
   PImage imgWater;
   PImage imgFuel;
   
   //Declare variables for initial game conditions
   int fuel = 0;
   int lives = 15;
   int score = 0;
   int currentLevel = 0;
   int timerLength = 60000;
   int endTime;
   boolean timerOn;
   boolean gameOver = false;
   boolean noKeys = false;
   
   void setup() {
     size(800, 600);
     frameRate(20);
     lives = 15;
     noCursor();
     f = createFont("Arial", 16, true);
   
     //Load the background image
     img = loadImage("road.jpg");
     imgCar = loadImage("car.jpg");
     imgSplash1 = loadImage("splash1.jpg");
     imgSplash2 = loadImage("splash2.jpg");
     imgSplash3 = loadImage("splash3.jpg");
     imgWater = loadImage("waterBG.jpg");
     imgFuel = loadImage("fuelCell.jpg");
   
     //Car starting positions, direction, and speed
     for (int i=0; i<cars.length; i++) {
       int x = (int)random(4);
       int speedIndex = (int)random(4);
       cars[i] = new Car(random(width), lanes[x], carSpeeds[speedIndex]);
     }
   
     //Fuel Cell starting positions
     for (int i=0; i<cells.length; i++) {
       cells[i] = new Fuel(random(width), random(60, height));
     }
   
     //Pirate starting positions
     for (int i=0; i<pirates.length; i++) {
       int pSpeedx = (int)random(8);
       int pSpeedy = (int)random(8);
       pirates[i] = new Pirate(random(width), random(60, height), pirateSpeeds[pSpeedx], pirateSpeeds[pSpeedy]);
     }
   
     //Player starting poition
     alien = new Player(400, 550);
   
     //Collectable ship parts position
     part1 = new Part(175, 150);
     part2 = new Part(620, 250);
     part3 = new Part(399, 350);
   }
   
   void draw() {
   
     if (currentLevel == 0) {
       level0();
     }
     else if (currentLevel == 1) {
       level1();
     }
     else if (currentLevel == 2) {
       level2();
     }
     else if (currentLevel == 3) {
       level3();
     }
     else if (currentLevel == 4) {
       level4();
     }
     else if (currentLevel == 5) {
       level5();
     }
     else if (currentLevel == 6) {
       level6();
     }
     else if (currentLevel == 7) {
       level7();
     }
     else if (currentLevel == 8) {
       level8();
     }
     else if (currentLevel == 9) {
       level9();
     }
     else if (currentLevel == 10) {
       level10();
     }
   }
   
   void gameOver() {
     textFont(f, 42);
     textAlign(CENTER);
     background(255);
     fill(0);
     text("GAME OVER", width/2, height/2);
     text("SPACEBAR TO RESTART", width/2, 350);
     if (keyPressed) {
       if (key == ' ') {
         currentLevel = 0;
         lives = 15;
         fuel = 0;
         score = 0;
       }
     }
   }
   
   //LEVEL 0
   void level0() {
     image(imgSplash1, 0, 0);
   
     if (mousePressed) {
       currentLevel = 1;
     }
   }
   
   //LEVEL 1
   void level1() {
   
     if (lives == 0) {
       gameOver();
     }
     else {
   
       if (score >= 3) {
         currentLevel = 2;
       }
       else {
   
         //Display game info
         image(img, 0, 0);
         fill(0);
         text("Lives: " + lives, 100, 35);
   
         //Initialise cars
         for (int i = 0; i < cars.length; i++) {
           cars[i].display();
         }
       }
       //Player dies if hit by a car
       for (int i = 0; i < cars.length; i++) {
         if (cars[i].intersect(alien)) {
           alien.die();
         }
       }
       //Initialise player 
       alien.show();
   
       //Initialise collectable parts 
       part1.appear1();
       part2.appear2();
       part3.appear3();
   
       //Check for player collecting ship parts 
       if (part1.intersect(alien)) {
         part1.collect1();
       }
       if (part2.intersect(alien)) {
         part2.collect2();
       }
       if (part3.intersect(alien)) {
         part3.collect3();
       }
     }
   }
   
   //LEVEL 2
   void level2() {
     image(imgSplash2, 0, 0);
   
     if (mousePressed) {
       currentLevel = 3;
     }
   }
   
   //LEVEL 3
   void level3() {
     currentLevel = 3;
     if (lives == 0) {
       gameOver();
     }
     else {
       if (fuel >= 1000) {
         currentLevel = 4;
       }
       else {
   
         noKeys = true;
         image(imgWater, 0, 0);
         alien.show2();
         if (currentLevel == 3) {
           endTime = millis() + timerLength;
           timerOn = true;
         }
   
         if (timerOn) {
           int remainingTime = endTime - millis();
           text("Time:" + remainingTime/1000, 400, 30);
   
           if (remainingTime <= 0 && fuel < 2000) {
             gameOver();
             timerOn = false;
           }
           else {
           }
         }
         fill(0);
         text("Fuel: " + fuel, 700, 30);
         text("Lives: " + lives, 100, 30);
   
   
         //Show fuel cells
         for (int i=0; i<cells.length; i++) {
           cells[i].showFuel();
         }
         for (int i=0; i<cells.length; i++) {
           if (cells[i].intersect(alien)) {
             cells[i].collect();
           }
         }
         //Show pirates
         for (int i = 0; i < pirates.length; i++) {
           pirates[i].display();
         }
         for (int i = 0; i < pirates.length; i++) {
           if (pirates[i].intersect(alien)) {
             alien.die();
             pirates[i].hit();
           }
         }
         for (int j = 0; j < pirates.length; j++) {
           for (int k = 0; k < cells.length; k++) {
             if (pirates[j].intersect(cells[k])) {
               cells[k].lose();
             }
           }
         }
       }
     }
   }
   //}
   
   //LEVEL 4
   void level4() {
     textFont(f, 42);
     textAlign(CENTER);
     background(255);
     fill(0);
     text("THIS IS LEVEL 4", width/2, height/2);
     text("SPACEBAR TO WIN", width/2, 350);
     if (keyPressed) {
       if (key == ' ') {
         currentLevel = 5;
       }
     }
   }
   
   //LEVEL 5
   void level5() {
     if (lives == 0) {
       gameOver();
     }
     else {
       //    if (hits >= 20) {
       //      currentLevel = 6;
       //    }
       //    else {
   
       noKeys = true;
       image(imgWater, 0, 0);
       alien.show2();
     }
   }
   //}
   
   //LEVEL 6
   void level6() {
     textFont(f, 42);
     textAlign(CENTER);
     background(255);
     fill(0);
     text("THIS IS LEVEL 6", width/2, height/2);
     text("SPACEBAR TO WIN", width/2, 350);
     if (keyPressed) {
       if (key == ' ') {
         currentLevel = 7;
       }
     }
   }
   
   //LEVEL 7
   void level7() {
     textFont(f, 42);
     textAlign(CENTER);
     background(255);
     fill(0);
     text("THIS IS LEVEL 7", width/2, height/2);
     text("SPACEBAR TO WIN", width/2, 350);
     if (keyPressed) {
       if (key == ' ') {
         currentLevel = 8;
       }
     }
   }
   
   //LEVEL 8
   void level8() {
     textFont(f, 42);
     textAlign(CENTER);
     background(255);
     fill(0);
     text("THIS IS LEVEL 8", width/2, height/2);
     text("SPACEBAR TO WIN", width/2, 350);
     if (keyPressed) {
       if (key == ' ') {
         currentLevel = 9;
       }
     }
   }
   
   //LEVEL 9
   void level9() {
     textFont(f, 42);
     textAlign(CENTER);
     background(255);
     fill(0);
     text("THIS IS LEVEL 9", width/2, height/2);
     text("SPACEBAR TO WIN", width/2, 350);
     if (keyPressed) {
       if (key == ' ') {
         currentLevel = 10;
       }
     }
   }
   
   //LEVEL 10
   void level10() {
     textFont(f, 42);
     textAlign(CENTER);
     background(255);
     fill(0);
     text("THIS IS LEVEL 10", width/2, height/2);
     text("YOU HAVE WON", width/2, 350);
   }
   
   //Player movement controls
   void keyPressed() {
     if (key==CODED) {
       if (!noKeys) {
         if (keyCode==DOWN) {
           alien.Down();
         }
         else if (keyCode==UP) {
           alien.Up();
         }
         else if (keyCode==LEFT) {
           alien.Left();
         }
         else if (keyCode==RIGHT) {
           alien.Right();
         }
       }
     }
   }
   
   Player alien;
   
   Part part1;
   Part part2;
   Part part3;
   

1. //Create fuel class
   class Fuel {
     float xF;
     float yF;
     //Fuel radius
     int fr = 20;
   
     Fuel(float posX, float posY) {
       xF = posX;
       yF = posY;
     }
   
     //Create show function for fuel
     void showFuel() {
       image(imgFuel, xF, yF);
     }
   
     //Specify intersect conditions for fuel and player
     boolean intersect(Player a) {
       float distance = dist(xF, yF, a.x_, a.y_);
       if (distance < fr + a.r + 10) {
         return true;
       }
       else {
         return false;
       }
     }
   
     //Create collect function for when player picks up fuel
     void collect() {
       xF = (random(width));
       yF = (random(60, height));
       fuel = fuel + 100;
     }
   
     //Create lose function for when pirates collide with fuel
     void lose() {
       xF = 1000;
       yF = 1000;
     }
   }
   
2. class Part {
     float x_;
     float y_;
     float d;
   
     Part(int posX, int posY) {
       x_ = posX;
       y_ = posY;
     }
   
   
     //Create appearance of first part
     void appear1() {
       d = 20;
       strokeWeight(1);
       smooth();
       fill(117, 203, 155);
       ellipse(x_, y_, d, d*2);
       fill(206, 206, 206);
       strokeWeight(2);
       ellipse(x_, y_-5, d/2, d/2);
       fill(255, 0, 0);
       strokeWeight(1);
       ellipse(x_, y_+5, d/4, d/4);
       ellipse(x_, y_+10, d/4, d/4);
     }
   
     //Create collect function for first part
     void collect1() {
       x_ = 700;
       y_ = 50;
       score++;
     }
   
     //Create appearance of second part
     void appear2() {
       smooth();
       triangle(x_+5, y_+4, x_+5, y_-10, x_+20, y_+15);
       triangle(x_-5, y_+4, x_-5, y_-10, x_-20, y_+15);
       fill(117, 203, 155);
       rectMode(CENTER);
       rect(x_, y_-2, 10, 12);
       fill(255, 255, 0);
       noStroke();
       triangle(x_-4, y_+4, x_+5, y_+4, x_, y_+18);
       fill(255, 68, 0);
       triangle(x_-2, y_+4, x_+3, y_+4, x_, y_+12);
     }
   
     //Create collect function for second part
     void collect2() {
       x_ = 745;
       y_ = 50;
       score++;
     }
     //Create appearance of third part
     void appear3() {
       fill(86, 86, 86);
       stroke(0);
       strokeWeight(1);
       triangle(x_, y_-10, x_-2, y_+8, x_+2, y_+8);
       fill(117, 203, 155);
       ellipse(x_, y_+7, 10, 4);
       ellipse(x_, y_-11, 4, 4);
     }
   
     //Creat ecollect function for third part
     void collect3() {
       x_ = 775;
       y_ = 50;
       score++;
     }
   
     //Specify intersect conditions for player and parts 
     boolean intersect(Player a) {
       float distance = dist(x_, y_, a.x_, a.y_);
       if (distance < d + a.r + 10) {
         return true;
       }
       else {
         return false;
       }
     }
   }
   
3. //Create class player
   class Player {
     int x_, y_, r;
   
     Player(int pXPos, int pYPos) {
       x_ = pXPos;
       y_ = pYPos;
     }
   
     //Create show function for player
     void show() {
       r = 15;  //Player size
       smooth();
       fill(255, 246, 180);
       stroke(0);
       strokeWeight(2);
       ellipse(x_, y_, r*2, r*2);  //Body
       fill(255);
       ellipse(x_-10, y_-5, 15, 15);  //Eye #1
       ellipse(x_+10, y_-5, 15, 15);  //Eye #2
       fill(0);
       ellipse(x_-10, y_-5, 7, 7);    //Pupil #1
       ellipse(x_+10, y_-5, 7, 7);    //Pupil #2
       fill(255, 0, 0);
       ellipse(x_-15, y_+ r, 18, 10);  //Foot #1
       ellipse(x_+15, y_+ r, 18, 10);  //Foot #2
   
       if (y_ < 50) {  //Prevent player from going off top of screen
         y_ = 50;
       }
       if (y_ > 550) {  //Prevent player from going off bottom of screen
         y_ = 550;
       }
       if (x_ <= 0 + r) { //Lose a life if player goes off left of screen
         alien.die();
       }
       if (x_ >= width - r) {  //Lose a life if player goes off right of screen
         alien.die();
       }
       if (x_ > 650 && y_ < 100) {
         x_ = 650;
       }
     }
   
     void show2() {
       x_ = mouseX;
       y_ = mouseY;
       r = 15;  //Player size
       smooth();
       fill(255, 246, 180);
       stroke(0);
       strokeWeight(2);
       ellipse(x_, y_, r*2, r*2);  //Body
       fill(255);
       ellipse(x_-10, y_-5, 15, 15);  //Eye #1
       ellipse(x_+10, y_-5, 15, 15);  //Eye #2
       fill(0);
       ellipse(x_-10, y_-5, 7, 7);    //Pupil #1
       ellipse(x_+10, y_-5, 7, 7);    //Pupil #2
       fill(255, 0, 0);
       ellipse(x_-15, y_+ r, 18, 10);  //Foot #1
       ellipse(x_+15, y_+ r, 18, 10);  //Foot #2
   
       if (y_ < 43 + r) {  //Prevent player from going off top of screen
         y_ = 43 + r;
       }
       if (y_ > 600 - r) {  //Prevent player from going off bottom of screen
         y_ = 600 - r;
       }
       if (x_ < 0 + r) { //Prevent player from going off left of screen
         x_ = 0 + r;
       }
       if (x_ > width - r) {  //Prevent player going off right of screen
         x_ = width - r;
       }
     }
     //Specify movement speeds for player 
     void Down() {
       y_= y_+100;
     }
   
     void Up() {
       y_= y_-100;
     }
   
     void Left() {
       x_= x_-30;
     }
   
     void Right() {
       x_= x_+30;
     }
   
     //Specify "respawn" point and die function 
     void die() {
       x_= 400;
       y_= 550;
       lives --;
     }
   }
4. 
   class Car {
     float xPos;
     int yPos;
     int speed;
     int cr = 15;
     Car(float tempXPos, int tempYPos, int tempSpeed) {
       xPos = tempXPos;
       yPos = tempYPos;
       speed = tempSpeed;
     }
   
     //Create move function for cars   
     void display() {
       image(imgCar, xPos, yPos);
       cr = 15;
       xPos = xPos +speed;
       if (xPos > width) {  //Cars reset if they go off screen
         xPos = 0;
       }
       if (xPos < 0) {
         xPos = width;
       }
     }
   
     //Specify intersect conditions for player and cars   
     boolean intersect(Player a) {
       float distance = dist(xPos, yPos, a.x_, a.y_);
       if (distance < cr + a.r) {
         return true;
       }
       else {
         return false;
       }
     }
   }
   
5. //Create pirate class
   class Pirate {
     float xPos;
     float yPos;
     float xSpeed;
     float ySpeed;
   
     //Pirate radius
     int pr = 20;
   
     Pirate(float tempXPos, float tempYPos, float tempXSpeed, float tempYSpeed) {
       xPos = tempXPos;
       yPos = tempYPos;
       xSpeed = tempXSpeed;
       ySpeed = tempYSpeed;
     }
     //Hit function for pirates when they collide with the player
     void hit() {
       xPos = random(width);
       yPos = random(60, height);
     }
   
     //Display function for pirates  
     void display() {
       image(imgCar, xPos, yPos);
       pr = 25;
       xPos = xPos + xSpeed;
       yPos = yPos + ySpeed;
       if (xPos > width) {  //Pirates reset if they go off screen
         xPos = 0;
       }
       if (xPos < 0) {
         xPos = width;
       }
       if (yPos > height) {
         yPos = 45;
       }
       if (yPos < 45) {
         yPos = height;
       }
     }
   
     //Specify intersect conditions for player and pirates 
     boolean intersect(Player a) {
       float distance = dist(xPos, yPos, a.x_, a.y_);
       if (distance <= pr + a.r + 5) {
         return true;
       }
       else {
         return false;
       }
     }
   
     //Specify intersect conditions for pirates and fuel
     boolean intersect(Fuel f) {
       float distance = dist(xPos, yPos, f.xF, f.yF);
       if (distance <= pr + f.fr ) {
         return true;
       }
       else {
         return false;
       }
     }
   }
   
   

1.       if (currentLevel == 3 && timerOn == false) {
2.         endTime = millis() + timerLength;
3.         timerOn = true;
4.       }

You can add a println() to the code to see that it correctly counts down with the changed code.