Automate through a remote desktop using selenium and AutoIt

I want to automate certain tasks which needs it to go through remote desktop. I will share the code which i wrote till now.

public class MainClass
{
  static WebDriverWait  wait;
  static WebDriver driver;
  public static void main(String args[])
  {
    driver = new HtmlUnitDriver(true);
    driver.get("https://mysite");
    WebElement submit_element=driver.findElement(By.id("Log_On"));
    driver.findElement(By.id("Enter user name")).sendKeys("my_username");
    driver.findElement(By.name("passwd")).sendKeys("my_password");
    submit_element.click();
    driver.findElement(By.id( "folderLink_0")).click();
    driver.findElement(By.id( "folderLink_2")).click();
    driver.manage().timeouts().implicitlyWait(100, TimeUnit.SECONDS);
    System.out.println(driver.getPageSource());
    driver.findElement(By.id("idCitrix.M")).click();
    System.out.println(driver.getPageSource());
  }
}

The line of code driver.findElement(By.id("idCitrix.M")).click(); opens the remote desktop in a new window.

The line System.out.println(driver.getPageSource()); is retrieving the same code in both places.

I believe this cannot be done solely by selenium. By browsing through the internet i learnt it is possible to do this using AutoIt. Any guidance is appreciated.Thank you.