How do I clear this setInterval inside a function?

the_int=window.clearInterval(the_int);

The setInterval method returns a handle that you can use to clear the interval. If you want the function to return it, you just return the result of the method call:

function intervalTrigger() {
  return window.setInterval( function() {
    if (timedCount >= markers.length) {
       timedCount = 0;
    }
    google.maps.event.trigger(markers[timedCount], "click");
    timedCount++;
  }, 5000 );
};
var id = intervalTrigger();

Then to clear the interval:

window.clearInterval(id);

// Initiate set interval and assign it to intervalListener
var intervalListener = self.setInterval(function () {someProcess()}, 1000);
function someProcess() {
  console.log('someProcess() has been called');
  // If some condition is true clear the interval
  if (stopIntervalIsTrue) {
    window.clearInterval(intervalListener);
  }
}