It's hard to believe with that much damage there was no indication of leaking on the inside.

Yikes

That is my question as well. A liner with any small imperfection can only serve to let moisture in causing it to rust from the inside.

This will give nightmares to anyone with an aftermarket roof rack.

This..for that much rust I'd expect you had water soaking the interior whenever it rained..

This scenario is the reason that I am not interested in installing an aftermarket roof rack. That being said, this looks like something more serious that improperly sealed mounting locations. Was this vehicle purchased new or used?

That looks more like chemical metal rejection 2 different metals reacting
I can’t see how fast water would rust your roof unless it was salted
Mike

All of these things, I'll grab the

pretty jacked up that some people are saying to fix it and dump it while hiding the damage.

Well what else can you do there, do you have any other suggestions? Cut a whole roof off of another vehicle and weld it on? Weld patches? I don't see either of those as a viable alternative so you either drive it until the rust perforations create so much mold that it's a health hazard, then scrap it (the honorable thing to do), or you dump it for cheap now. Perhaps it's fixable but it doesn't look like it to me.

I have never sold or traded in a vehicle with issues like this but I'm not sure what else can be done here. Send it to auction and the buyer that gets it cheap gets it cheap for a reason. Happens all the time. More often than I'd like to think. Probably no worse than a previously flooded vehicle.

Its one thing to trade it in while being up front about the damage.

One could probably bondo it, respray the section and trade it in which is highly screwed up to do.

Cutting the roof off and welding in a new roof would fix the problem but would be a pretty costly solution. Might be able to find a junkyard and weld in new roof sections as well but i'm not sure how well that would go.

Surprisingly a new roof isn't that expensive but the body shop hourly rate would be: Roof & Components for 2013 Toyota 4Runner | Camelback Toyota Parts

Learn how to weld.

Would the roof skin alone like that even be enough? I'd think you would have to replace all the parts the rust is creeping into as well.

Whats done is done.If you trade it in or sell it (be upfront). you probably wont get much for it.Take it to a body shop that deals with classic restoration and ask them to evaluate it and see what it costs. If you can afford it get it fixed and make it your forever vehicle or cut your losses and move on. In either case it's going to be costly.

I really want a rack, but this got me scared as he!! now. Did you see any damage to the inside headliner at all that would indicate any issues? I would assume with that much damage that you should have started see water issues in the headliner or at the inside starting to smell all the time.

Also, is there a reason that you removed the rack multiple times in the past? I had a rack on my last 4runner for over 6 years (parked outside) and never once thought about removing the rack once it was already up there.

In the pictures it appears the inside of the roof is scraped away as if a grinder was used on it. The bolts and brackets also appear to be a mis-matched set. Did you have to drill new holes and such for the full length rack? If so, did you repaint the cut metal to protect it or just seal with permatex?