Gently peel back the plastic cover from the inside of the door. Be careful with this, apart from keeping dust out, it keeps water in the door that has gotten past the window seals and stops the water coming into the car, so it needs to be sealed back as best you can afterwards.
Looking back into the door, the pic below on the left shows the rod and (yellow)clip as it should be, the pic on the right shows how the (white) clip has broken allowing the rod to drop down into the path of the window mechanism. If you wind the window down, it will catch on the rod and either bend it, or break it right off at the lower end - which then becomes a serious repair job. The one on the right has actually been caught by the window, but as the window wasn't wound right down, it is only bent a little where it connects to the lock mechanism at the back of the door.
Here is a pic of a broken one thanks to Jarrod.
This is a new passenger clip (left) and broken drivers clip (right). I bought 2 new clips at the same time, different part numbers for each side of the car and my new drivers one was also white and the passengers was yellow so I figured they were colour coded that way. Parts available from Toyota. 69293-12050 Drivers side, 69293-12060 Passengers side. The pic above from inside Tam's drivers door shows a yellow one however.
Fortunately I was able to just bend my rod back into place, fit a new clip over the end, locate it into the hole in the handle then snap lock it into place.
If your rod has broken off, you need to remove the mechanism entirely which is a much longer and fiddly job (anyone have a tutorial?) then either get the rod welded up, replace it, or replace the entire mechanism.
In Tam's car, the problem was different.
Here are the notes and pics from Theo from GT Autosound, but I am not too sure what rod on the left he is referring to.
"If you notice there is a metal rod just to the left that is bent around. This is slightly loose and can cause the rod to get caught behind the release which means it cannot move and gets stuck. This in turn means that it won’t release the lock when you lift the handle. Only way to fix this is to remove the rod and re-bend this back into shape. Make sure it is secure and not lose when you -install."