It links to another deleted scene.

As you will remember from the final film, the two Jedi split up and hide in separate ships (which is a daft idea when you think of it, they could have ended up on opposite ends of the planet but I digress).

Obi-Wan ends submerged under water and doing an homage to a scene from Apocalypse Now.

If I remember correctly the water screws up Kenobi's lightsaber so Qui-Gon has to take out the droid instead.

Qui-Gon gives his pupil a bit of a ticking off about getting his weapon moist.

The BBC did a special (it might have been an Horizon or an Arena special) to tie in with the release of TPM and you see the scene being shot.