It happens: just when you think it’s safe to update macOS, it turns round and bites you on the bum. Instead of getting the latest, fixed and sweet-running version, the App Store dumps its ghost on you, and macOS is staggering along looking like it’s half dead. So what do you do next?

The first and most important action is not to rush at trying to fix it, or give up in disgust and start reverting to the last version you were running. Updating macOS is one of the most complex things that happens to your Mac. Although mis-updates used to be quite common in the past, they do still occur now, even with all the checks that take place. If you were just about to go out, for example, don’t rush at anything in a panic. If macOS does really seem messed up, shut down or leave your Mac until you have counted to a hundred, had a strong cup of your favourite beverage, and have worked out what to do next.

When you’re ready, the best thing to try next is to start up in Safe mode, which is explained in full here. We often don’t do that properly, and it is worth following Apple’s instructions very carefully:

1. If your Mac is not already shut down, shut it down, and wait 10 seconds before pressing the Power Button to start it up; restarting is not a good way to get this to work properly!
2. As soon as you hear the startup chime/chord, press and hold down the Shift key on your keyboard.
3. Once the grey Apple logo and progress bar appear, you can release the Shift key.

This does two things which are likely to help: it clears a lot of caches and other things which could be causing your problems, and it disables third-party extensions which could also be an issue.

If Safe mode seems to fix the update so that most things are working properly again, and you can’t think of any incompatible extensions etc., then try restarting back into normal mode. If your problems recur, then the chances are that you have a third-party extension or service which is incompatible, and you need now to turn off all suspects, to try to isolate the one that is at fault.

If Safe mode makes little or no difference, the next thing to try is downloading a standalone version of the update and installing that. If this was a macOS update, you should make this the latest Combo updater, as detailed here. Locate that updater by searching Apple’s Support section, with the macOS version that you need and the word ‘combo’ as your search term, e.g. ‘10.11.6 combo’. Sierra 10.12.6 Combo updater is available from here.

If that fixes your problems, you will also need to bring it up to date with respect to any ‘silent’ security and other updates. If you refuse to use Terminal, you may be able to force that by opening the App Store pane, unchecking the Install system data files and security updates item, switching to another pane, then back to the App Store pane. Turn that item back on, then click on the Check Now button below.

If you’re prepared to type in a command in Terminal, enter the following command from an admin user account:
sudo softwareupdate --background-critical
press Return, then at the prompt, enter your admin account password. Terminal will then report something like
softwareupdate[1587]: Triggering background check with forced scan (critical and config-data updates only) ...
Once those updates have occurred, they will be reported in the Installations item of System Information. Sometimes they can take a while to happen.

If none of these sorts your problems out, then there are still plenty of other things which you can try before admitting defeat and going back to the last version of macOS. These include starting up in Recovery mode and running First Aid from Disk Utility there on your startup volume, and resetting the SMC and NVRAM.

There are two other things to bear in mind. It is often worth opening the App Store app again after you have applied a macOS update to see if there are further updates to come. It is not unusual, for example, for Apple to have to fix things in macOS Server or other software after a macOS update, and any such updates should be offered to you once you have updated macOS itself.

The other is that it might be a hardware issue, either with your Mac or with a connected peripheral. Hardware faults in Macs can sometimes wait for a macOS update before making themselves known, so you could perhaps run Apple Hardware Test or Diagnostics, detailed here. You can eliminate peripherals from the question by shutting down and disconnecting all non-essential peripherals, ideally leaving just a wired USB mouse/trackpad and wired keyboard, any required display, and your network connection.

Remember, if you have Apple’s rechargeable wireless keyboard or trackpad, you can turn those into wired devices by simply plugging their charging cables into a USB port on your Mac. If you only have Apple’s rechargeable wireless mouse, you will need a wired USB mouse to use instead, as you can’t use the Apple mouse while the recharging cable is connected.

One potential source of information during all this are the log entries in Sierra’s or High Sierra’s unified log. You cannot browse what happens during startup, though, using Apple’s bundled Console alone, as it doesn’t show you any entries from the past. There are two solutions: you can either use the log command in Terminal to export a logarchive and browse that in Console, or you can use my free log browser Consolation, available in Downloads above.

Sierra’s log contains a great deal more than in previous versions of OS X, sometimes tens of thousands of entries each minute. There’s a guide to what you can see during startup here.

You might also find it helpful to consider whether you may have a munged preference file or permissions. I explain where those are in Sierra here. However, they are normally only responsible for little niggles, not complete failures of obvious functions in maOS. This article explains how Sierra may benefit from repairing permissions, although that is very different from in older versions of macOS.

Another trick which sometimes comes in handy is to create a new user account, preferably with admin rights, and try starting up with that account. If your problems vanish, then it makes it extremely likely that your problems are caused by something – such as a startup item, LaunchAgent, or LaunchDaemon – in your normal Home folder.

You may well not be alone in your problems. I keep a running list of known bugs in macOS Sierra 10.12.6 here, and soon after the first official (non-beta) release of macOS High Sierra is released, I will start another article covering that. Apple’s support discussions are sometimes a great help too, and you can always call or tweet Apple support @AppleSupport, or arrange an appointment at your nearest Genius Bar.