To use commandline arguments, just use args[0] args[1] etc.. So in your example "3 HELLOWORLD" - 3 is args[0] and HELLOWORLD is args[1].
As shift is an integer you must parse it which converts it from a String to an Integer. To improve the code, you should catch any errors incase the String entered cannot be converted.
    public static StringBuffer rotate(int shift, String plainText){
    StringBuffer result= new StringBuffer();
    for (int i=0; i<plainText.length(); i++){
        if (Character.isUpperCase(plainText.charAt(i))){
            char ch = (char)(((int)plainText.charAt(i) + shift - 65) % 26 + 65);
            result.append(ch);
        }
        else{
            char ch = (char)(((int)plainText.charAt(i) + shift - 97) % 26 + 97);
            result.append(ch);
        }
    }
    return result;
}
public static void main(String[] args){
    String plainText = args[1];
    int shift = Integer.parseInt(args[0]);
    System.out.println("Text  : " + plainText);
    System.out.println("Shift : " + shift);
    System.out.println("Cipher: " + rotate(shift, plainText));
}
This is the output after using the arguments you mentioned