Vatican in the afternoon?

The Basilica and the Museums are two different things. There's quite a walk between them. Each has its own security/entry line. The Basilica is free, and there's no way to go directly from the Basilica to the Museums. In the past, commercial tours covering both venues were allowed (usually) to use a door between the Sistine Chapel/Museums and the Basilica. That avoided the security line at the Basilica and eliminated a lot of walking. It's highly unlikely anyone not on a combo tour would be able to use that door, and it cannot be used in reverse (you can't start in the Basilica and then scoot into the Sistine Chapel/Museums)

During peak season the Vatican Museums are open later one or two nights a week--though the Museums recently extended their regular hours, so the difference isn't as great as it used to be. In the past, a very few people mentioned somewhat less crowding when they took advantage of the late hours. When is your trip?

There is a general pathway through the Museums with a few opportunities to bypass things you're not interested in. With time and determination, I was able to backtrack to see the Pinacoteca, but it was like swimming upstream.

Have no illusions; you'll be sharing the Vatican Museum experience with many, many other people.

From comments posted on this forum, I understand showing up at St. Peter's before it opens (usually at 7 AM, I believe) will give you a relatively short/quick security line to deal with. I think that's by far the best way to see St. Peter's.

Thanks, acraven. I’m traveling early September. I read they no longer have the early entry tours since they changed opening hours from 9 to 8 but hopeful they will provide a new option between now and then. I’m on the fence if I’m better off doing their guided (internal tour) or just doing the RS audio guide do we can skip what is not of interest. My understanding that all tickets are timed entry so that if we opt to buy individual tickets (non-guided) and do the audio guide, we only have to deal with the security line but would still have to go around to the basilica and do that line, too.

The line for the Museums isn't bad at all if you have pre-purchased your entry. You'll have to line up again inside to convert your reservation into an actual ticket (unless they've changed their procedures since last March). The issue is the conditions once you get inside.

I think I remember a few comments about the Museums getting warmer as the day goes on (all the body heat doesn't help), but I can't comment on that myself since my visit was in March. If that really is an issue, it would argue against arriving at 1 or 2 PM, I guess.

I used the audio guide and have no experience with VM tours. Rick has a lot of details in his guidebook. Reading through the VM section at least once ahead of time, then consulting it as needed during your visit, could be all you need.

On any given day, some rooms in the Museums will be closed off, which could cause a change in the route they set up.

I highly recommend going through the Vatican Museum as early as you can. Last month I went with a tour that went in right at opening time, and the crowds are MUCH less than they are later in the day. The whole experience is much more enjoyable. The Sistine Chapel, while it did have people inside, did not have the crowds that are in there later in the day. (I did the same tour two days in a row, first day at 8am, the next day at 1pm. I much preferred the earlier tour)