I think it was a japanese animated series. In the series a humanoid alien civilization is dying out, but they don't understand why. They discover Earth and notice that humans don't have the same problem. So aliens decide to investigate humans.
The investigation goes like this: aliens board a ship, shrink themselves and their ship to microscopic levels, enter human body, disable some random organ and observe the result (what a genius plan!). The human subject collapses and everyone is very sad.
But (surprise-surprise!) humans also have the shrinking technology, so they board their own ship, shrink themselves to the same size as aliens, enter the suffering person's body, fight the aliens (with lasers!) and undo the damage (or cause more damage themselves, my memory fails me here).