The heartbreak of just-noticed rust!!
 

Our 2009 4Runner has been insanely reliable and I've kept the bottom oil-undercoated for years and it looks to be in perfect shape. However, today I noticed rust coming up through the top of the driver's-side door sill. What's the best way to fix this? The car looks to be in mint condition other than this spot of rust. Or is this a bellwether that portends a lot more rust coming up, and it's not worth fixing?

Its surface rust on a 15 year old car. You're fine. I'm guessing you got a rock chip that caused some rust to bubble up.

Get a paint pen, scratch off paint/rust with the provided ceramic tip, touchup with paint, then apply clearcoat.

I'd pull both sill plates and see what's under them. My guess is that by the looks of the rust following the moldings edge, there's more under there. Also, I'd get under the vehicle and look at the bottom and back side of the rocker and the floor, there might be more and it's moving up. There's a few ways it can start in that spot, it's from underneath or for some reason that area was not treated properly from the factory and water is collecting there or you have a water leak somewhere on that side and it's growing.

Pop that cover off and see how it looks. Seems to me it would be an easy fix and may just have gotten scratched by shoes with sand on them. The really bad stuff to worry about is not on the body of the vehicle. I would gladly trade for that. :)

That's actually a very common place for 4Runners and Tacomas to rust, The bottom edge of the plastic rocker panel cover is actually sharp and eventually wears through the paint on the steel rocker panel. If you happen to live where they use road salt, it can get under the plastic panel and start to corrode the steel as soon as the paint wears through. You don't see the rust starting because it's covered up - until it's too late.

What can you do about it? The best fix is to take it to a collision shop you can trust and have them pull the plastic panel off, remove the rust and repaint the area. Next, have them dull down the sharp bottom edges on the plastic and add PPF as I did (to all four doors) as shown below. This will prevent it from happening again.

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id pop the cover off and sand the rust off, touch up paint and clear coat it, get to it fast, i had another car that had a tiny spot like this, after 1 year of procrastinating it grew like 2 inches