Fading led with push button

The main problem is you have to reset brightness to 0 when the switch is LOW. Btw, I did not test the sketch, only compiled it.

int led = 9;          
int brightness = 5;    
int fadeAmount = 5;    

void setup() {
   Serial.begin(9600);
    pinMode(led, OUTPUT);
}
void loop() {
  int val = digitalRead(2);
  Serial.println(val);
if (val==HIGH){
  analogWrite(led, brightness);
  brightness = brightness + fadeAmount;
  if (brightness <= 0 || brightness >= 255) {
    fadeAmount = -fadeAmount; }
  delay(100);
}
else{ 

  digitalWrite(9, LOW);
  brightness = 0;    // Restart with brightness 0
}
}

Some other improvements result in:

#define LED_PIN      9  
#define DELAY_TIME 100        
int brightness = 5;    
int fadeAmount = 5;    

void setup() {
   Serial.begin(9600);
   pinMode(LED_PIN, OUTPUT);
}

void loop() {
  int switchButton = digitalRead(2);
  Serial.println(switchButton);

  if (switchButton == HIGH) {
    analogWrite(LED_PIN, brightness);
    brightness += fadeAmount;
    if ((brightness <= 0) || (brightness >= 255)) {
      fadeAmount = -fadeAmount; 
    }
    delay(DELAY_TIME );
  }
  else { 
    digitalWrite(LED_PIN, LOW);
    brightness = 0;    // Restart with brightness 0
  }
}

Explanation

1. Always indent your code (so that { and } are clear, notice each new { increases the indentation by two spaces, each } decreases the indentation by two spaces.
2. For values that do not change use a #define. This prevents (in this case) a few bytes not be stored in valuable memory space. Especially if you would use arrays this is important.
3. You used 9 in digitalWrite(9, LOW); which was probably a mistake, always use defines wherever possible. I also would use #define DELAY_TIME 100 instead of the hardcoded 100 value.
4. I addes some spaces before/after values (like switchButton == HIGH). It doesn't matter if you do or not, but be consequent.
5. Use good variable names (switchButton is more clear than val.
6. Use brightness += fadeAmount; instead of brightness = brightness + fadeAmount;; this is the normal way of increasing (or decreasing/multiplying/whatever) the value of a variable.
7. Use ( and ) in non trivial if statements like if ((brightness <= 0) || (brightness >= 255)), this could save you hours of searching in case you ever make a mistake (in this case there is no functional change).

Good luck with your project.