I've been following the comments here, as this is one of the few places on the Internet where MRT 1.68 problems are being discussed. Much thanks to hoakley at https://eclecticlight.co/2020/10/19/apple-has-pushed-updates-to-xprotect-and-mrt-17/ and others who have contributed to several solutions that have worked for me. In building this guide, I've borrowed liberally from others posts. Thank you all.
My OS: El Capitan 10.11.6
My machine: MacPro5,1
Three approaches have been successful for me in stopping the rampant CPU use by MRT.app. One requires installing another utility (App Tamer), and the other two require some command line wizardry. I'll summarize each one below.
First Approach: APP TAMER
1. Download App Tamer from the St. Clair Software site:
www.stclairsoft.com/AppTamer/
2. Install and in App Tamer's interface find MRT and check the box to "Stop this app completely."
If this works for you, nothing else is needed. When Apple fixes the problem, you can simply uncheck the box and the new version of MRT can do it's job.
Second Approach: Replace MRT.app 1.68 with a previous version
1. Obtain an older version of MRT.app from Time Machine or another backup. (I used 1.67).
2. Restart while holding down Command-R to boot into macOS Recovery.
3. Start Terminal from the Utilities menu.
4. Disable SIP from the command line:
csrutil disable
5. Exit Terminal and open Disk Utility. Find your boot drive in the list and unlock and mount it if necessary.
6. Exit Disk Utility and return to the terminal.
6. Delete the old copy of MRT.app:
rm -fR /Volumes/YourBootDrive/System/Library/CoreServices/MRT.app
7. Copy old version of MRT.app to the system:
cp /path/to/old/version/MRT.app /Volumes/YourBootDrive/System/Library/CoreServices/MRT.app
8. Re-enable SIP:
csrutil enable
9. Restart
10. VERY IMPORTANT: without this step the OS will reinstall MRT with the current version within hours. Immediately after restarting to your normal desktop, if you use El Capitan open System Preferences > App Store and uncheck "Install system data files and security updates." In other Mac OS versions you may need to do this in the Software Update pane. (Put a sticky on your screen to remind you to re-enable this when Apple has resolved the problem.)
Third Approach: Disable MRT.app by removing executable permissions
1. Restart while holding down Command-R to boot into macOS Recovery.
2. Start Terminal from the Utilities menu.
3. Disable SIP from the command line:
csrutil disable
4. Exit Terminal and open Disk Utility. Find your boot drive in the list and unlock and mount it if necessary.
5. Exit Disk Utility and return to the terminal.
6. Remove executable permissions from MRT.app:
chmod -R -x /Volumes/YourBootDrive/System/Library/CoreServices/MRT.app
7. Re-enable SIP:
csrutil enable
8. Restart
9. VERY IMPORTANT: without this step the OS will reinstall MRT with the current version within hours. Immediately after restarting to your normal desktop, if you use El Capitan open System Preferences > App Store and uncheck "Install system data files and security updates." In other Mac OS versions you may need to do this in the Software Update pane. (Put a sticky on your screen to remind you to re-enable this when Apple has resolved the problem.)
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Finally, if you are having issues with MRT.app 1.68, released in Mid October, 2020, please report the issue to Apple. Please go to https://feedbackassistant.apple.com and report the issue, if you are a developer, or https://www.apple.com/feedback/macos.html if you are not a developer.
The more reports they get about MRT using massive amounts of CPU the quicker it will get fixed.
Thank you.