It’s the last port of call. You’ve tried everything else, including installing the latest Combo updater package, and nothing has fixed your problem. There’s only one thing for it, to re-install macOS.

Should that be an install, re-install, or clean (re-)install? Just what is the difference now, and which should you do?

Recent versions of macOS, particularly those from Sierra onwards, feature System Integrity Protection (SIP), which blocks the user or any other userland software – even when running as root – from tampering with the great majority of system files, including bundled apps like Chess. Only an installer signed by Apple itself can replace the many files and folders now protected by SIP. So whichever you try, you’ll be running an Apple macOS installer.

Before you try anything, it’s essential that you have good backups, preferably at least two current, such as a mirror copy of you startup disk and your last Time Machine backup. Even if you’re going to try the most minimal (re-)install, you must be prepared to have to restore all or any of you apps, documents, and other files, and for a clean (re-)install, they will be essential.

You can install macOS using any of three techniques:

• By downloading the current installer app from the App Store, and running that.
• By making a bootable USB memory ‘stick’ installer using the current macOS installer, creation of which is described here.
• In Recovery mode, which is described here.

Of those, only the third is recommended by Apple as a means of replacing the existing installation of macOS, which is why it should strictly be referred to as re-installing macOS, as there’s already a copy in place, which you’re trying to ‘fix’.

The next decision to make is which version of macOS to re-install. Generally, you’ll want the same version that you have just been running, in which case you should start up in regular ‘local’ Recovery mode using ⌘R (Cmd-R). This is best done using a wired (USB) keyboard and mouse/trackpad; some Macs don’t run reliable connections to Bluetooth peripherals until late during startup, and may not detect the startup key combination in time to enter Recovery mode reliably.

You also have two other options for Recovery mode: ⌥⌘R (Opt-Cmd-R) and ⇧⌥⌘R (Shift-Opt-Cmd-R), which install the latest version of macOS which is compatible with your Mac, or the original version of macOS which shipped with it, respectively. These aren’t usually appropriate when you’re aiming to re-install macOS.

The other essential decision to be taken now before starting the process is whether to perform a ‘clean’ re-install. This used to be more valuable in the days before SIP, but still has its uses.

There are plenty of system files which aren’t protected by SIP, largely because they are written to during normal use. Databases and other stores can cause many problems, and replacing them with fresh ones might fix your Mac. Only by wiping the old system files completely can you be confident that your Mac will start with a clean sheet – and that can be good grounds for going the extra mile in a ‘clean’ re-install.

There isn’t an option in Recovery mode to perform a clean re-install. To do that, you have to open Disk Utility and there erase your startup volume, then re-install macOS onto it.

If you re-install macOS without the clean step, you shouldn’t have to re-install all your apps and your Home folder, and the time required isn’t as long. If you opt for a clean re-install, then you will have to migrate apps, Home folder, settings and everything else from your latest backup, and that will take a long time.

There is another danger with a clean re-install. If the problem that you’re trying to fix isn’t in macOS at all, but in something else which you have installed, when you migrate your files back onto your Mac after the re-install, you could also be re-installing whatever created the problem in the first place.

There is one occasion when you should always opt for a clean re-install, and that’s when you’re preparing your Mac for disposal, as I have detailed here.

Re-installing macOS should be something you do only when everything else has failed to fix the problem. Some operating systems appear designed to be re-installed every few months, but macOS is not like that, and SIP makes it less likely that a re-install will do anything to help. There are plenty of generic solutions, such as installing the latest Combo update, or creating a new user and seeing if that too suffers the same problem, which can lead you to a better solution. But there are times when it’s the only answer.

Finally, once you have got your re-installed and re-invigorated macOS up and running, ensure that it’s up to date with the latest security updates, which normally aren’t rolled into the system installers. One simple way of doing that is to open my free LockRattler and click on its List all pending updates button, then install them with the button below that.