I changed batteries and it now just sits on the menu screen.

Does the light on the ATV blink when you hit a button?

If so, the remote is trying to talk to the ATV.

If not, the remote is not working at all.

If the light blinks and particularly if it does 3 times for each press, the ATV is ignoring it.

Simply un-pair the remote:

Pair or unpair your Apple Remote with your Apple TV (3rd generation or earlier) - Apple Support

Obviously use the second method specified since you can't navigate the menus.

No blinking means the remote is broken or the battery is dead.

There is a remote possibility the ATV is frozen. Pull the power plug for 1 minute then replug and see if it boots normally.

If it boots Ok and still does not blink on button press, consider getting another battery or remote.

Also you mention about using the iPad. If the remote app controls the ATV normally, then it is all remote...