Final Monster, Item and Room Maps.

public static void main(String[] args){
  Room[][] Map = new Room[5][5]; {
   Map[0][0] = new Room("Rm1", true, false, true, false, true);
   Map[0][1] = new Room("Rm2", true, true, true, false, false);
   Map[0][2] = new Room("Rm3", true, true, true, false, false);
   Map[0][3] = new Room("Rm4", true, true, true, false, false);
   Map[0][4] = new Room("Rm5", false, true, true, false, false);
   Map[1][0] = new Room("Rm6", true, false, true, true, false);
   Map[1][1] = new Room("Rm7", true, true, true, true, false);
   Map[1][2] = new Room("Rm8", true, true, true, true, false);
   Map[1][3] = new Room("Rm9", true, true, true, true, false);
   Map[1][4] = new Room("Rm10", false, true, true, true, false);
   Map[2][0] = new Room("Rm11", true, false, true, true, false);
   Map[2][1] = new Room("Rm12", true, true, true, true, false);
   Map[2][2] = new Room("Rm13", true, true, true, true, false);
   Map[2][3] = new Room("Rm14", true, true, true, true, false);
   Map[2][4] = new Room("Rm15", false, true, true, true, false);
   Map[3][0] = new Room("Rm16", true, false, true, true, false);
   Map[3][1] = new Room("Rm17", true, true, true, true, false);
   Map[3][2] = new Room("Rm18", true, true, true, true, false);
   Map[3][3] = new Room("Rm19", true, true, true, true, false);
   Map[3][4] = new Room("Rm20", false, true, true, true, false);
   Map[4][0] = new Room("Rm21", true, false, false, true, false);
   Map[4][1] = new Room("Rm22", true, true, false, true, false);
   Map[4][2] = new Room("Rm23", true, true, false, true, false);
   Map[4][3] = new Room("Rm24", true, true, false, true, false);
   Map[4][4] = new Room("Rm25", false, true, false, true, false);
   }
 
 
 
   Monster[][] MonMap = new Monster[5][5];{
  
   MonMap[0][0] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[0][1] = new Monster(15, 10, " Evil (Abed) Warlock");
   MonMap[0][2] = new Monster(35, 4, " Flatulant Old One");
   MonMap[0][3] = new Monster(40, 2, " Doppleganger Of Changception");
   MonMap[0][4] = new Monster(50, 9, " Brittanica The Protester");
   MonMap[1][0] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[1][1] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[1][2] = new Monster(42, 6, " Dean The Dalmatian");
   MonMap[1][3] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[1][4] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[2][0] = new Monster(10, 40, " The Great Rooory Train");
   MonMap[2][1] = new Monster(10, 40, " Hami The Destructive");
   MonMap[2][2] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[2][3] = new Monster(100, 5, " Irregular Mass");
   MonMap[2][4] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[3][0] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[3][1] = new Monster(150, 20, " Adamus The Destroyer");
   MonMap[3][2] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[3][3] = new Monster(20, 30, " MAD DOG!");
   MonMap[3][4] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[4][0] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[4][1] = new Monster(40, 10, " D-d-d-d-odds");
   MonMap[4][2] = new Monster(30, 5, " Miscellanous Grunt");
   MonMap[4][3] = new Monster(40, 7, " Mac");
   MonMap[4][4] = new Monster(150, 10, " The Dark Destroyer");
}


  Item[][] ItemMap = new Item[5][5];{
  
   ItemMap[0][0] = new Item(true, "Prop");
   ItemMap[0][1] = new Item(false, "Books");
   ItemMap[0][2] = new Item(true, "Hourglass");
   ItemMap[0][3] = new Item(true, "Pen");
   ItemMap[0][4] = new Item(false, "Birdcage");
   ItemMap[1][0] = new Item(true, "Hipflask");
   ItemMap[1][1] = new Item(true, "CD");
   ItemMap[1][2] = new Item(true, "Candle");
   ItemMap[1][3] = new Item(true, "Battery");
   ItemMap[1][4] = new Item(false, "Decorative Sword");
   ItemMap[2][0] = new Item(false, "Gold Ring");
   ItemMap[2][1] = new Item(false, "Diary");
   ItemMap[2][2] = new Item(true, "Pocketwatch");
   ItemMap[2][3] = new Item(false, "Bird Feather");
   ItemMap[2][4] = new Item(true, "Coins");
   ItemMap[3][0] = new Item(false, "Memory Stick");
   ItemMap[3][1] = new Item(false, "DVD");
   ItemMap[3][2] = new Item(false, "Dog Collar");
   ItemMap[3][3] = new Item(false, "Spoon");
   ItemMap[3][4] = new Item(false, "Perfume Bottle");
   ItemMap[4][0] = new Item(false, "Papers");
   ItemMap[4][1] = new Item(false, "Pendant");
   ItemMap[4][2] = new Item(false, "Marbles");
   ItemMap[4][3] = new Item(false, "Crown");
   ItemMap[4][4] = new Item(false, "Warhammer");
  
  
  
  }
 
  Item[] inventory = new Item[5];{
   inventory[0] = new Item(false, "Empty");
   inventory[1] = new Item(false, "Empty");
   inventory[2] = new Item(false, "Empty");
   inventory[3] = new Item(false, "Empty");
   inventory[4] = new Item(false, "Empty");
  }

Battle System

I have finally after a few weeks of testing and iteration come out with a working battle system for the project.

if(UserInput.equals("BATTLE")){
  
     System.out.println(MonMap[x][y].name + " Attacks for " + MonMap[x][y].damage);
     System.out.println("You now have" + PHealth);
   
   Boolean EnemyDefeated = false;
   System.out.print("You are now battling " + MonMap[x][y].name);
   System.out.print("What would you like to do?");
  
   while(EnemyDefeated ==  false){
   UserInput = input.nextLine();
   UserInput = UserInput.toUpperCase();
    if(UserInput.equals("ATTACK")){
     MonMap[x][y].hp = MonMap[x][y].hp - PDam;
     System.out.println("You attack the monster for " + PDam + " points of damage");
     System.out.println();
      if(MonMap[x][y].hp <= 0){
      Map[x][y].RmClr = true;
      EnemyDefeated = true;
      PScore = PScore + 10;
      System.out.print("The enemy has been defeated");
       if(PScore >= 250){
        System.out.println("You have completed the game, well done");
        System.exit(0);
       }
      }
    }
   
    if (UserInput.equals("KILL")){
     MonMap[x][y].hp = 0;
     Map[x][y].RmClr = true;
    }
    if(UserInput.equals("RUN")){
     System.out.print("In which direction would you like to run?");
     UserInput = input.nextLine();
     UserInput = UserInput.toUpperCase();
      if(UserInput.equals("NORTH")){
       y = y + 1;
       EnemyDefeated = true;
      }
      if(UserInput.equals("SOUTH")){
       y = y - 1;
       EnemyDefeated = true;
      }
      if(UserInput.equals("EAST")){
       x= x + 1;
       EnemyDefeated = true;
      }
     
      if(UserInput.equals("WEST")){
       x = x - 1;
       EnemyDefeated = true;
      }
    }
   
     PHealth = PHealth - MonMap[x][y].damage;
      if(PHealth <=0){
       System.out.println("I am afraid you have died, please try again.");
       System.out.println("The game will now return to the beggining");
       for(int i=0;i<=4;i++){
        Map[i][1].RmClr = false;
        Map[i][2].RmClr = false;
        Map[i][3].RmClr = false;
        Map[i][4].RmClr = false;
        PScore = 0;
        x=0;
        y=0;
       }
      }   
}
}