[Xiaomi Redmi Note 3 Guides, News, & Discussion] ameeno:
Dwl99 put a great guide together, the link is here:

http://xdaforums.com/redmi-note-3/how-to/guide-redmi-note-3-special-edition-kate-t3523371

Another guide I found useful is http://en.miui.com/thread-363264-1-1.html

Full URL of original post is:

https://forums.whirlpool.net.au/forum-replies.cfm?t=2566258&p=6&#r120

Now, I did it in a slightly different way, I prefer my way because I believe it is safer but here goes:

0. Update Miui to latest version Using the OTA update or Fastboot/Miflash method mentioned above. (I have a guide in this thread)

Once up to date:

1. Unlock the boot loader using the official method, this can take two 2 three days using en.miui.com/unlock/

Download the unlock tool. - Enable unlock boot loader options in developer options on MIUI (This can be done by tapping 10 times quickly on "Miui Version" in the about phone section of the phone. After this, go to additional settings >Developer options > enable developer options and unlock boot loader.

Next simply follow the guide on the MIUI unlock tool to unlock boot loader.

2. Flash TWRP ZCX Version: http://xdaforums.com/redmi-note-3/how-to/zcx-twrp-install-twrp-flash-supersu-t3462448

This version of TWRP allows you to see and backup ALL partitions of your Xiaomi device.

Make sure you boot into this TWRP after flashing so it sticks (otherwise your phone will not boot)

Use the settings to back up ALL partitions to your EXTERNAL SD card. Keep that safe for the future in case you break your phone or lose imei or whatever.

I recommend transferring this backup to a PC or desktop. - Once this is done, you can breathe easy, you will always have a complete full backup of your device should you break it, you can relax in the future.

3. After backing up all of the partitions to the external SD card:

Download some files on https://forums.whirlpool.net.au/forum-replies.cfm?t=2566258&p=6&#r120

The 4 main files you need are: 1 CM13 rom file, 2 TWRP Cofface Version, 3 the KATE version of CM13 firmware files (Whirlpool has this on his guide at the bottom edit) and 4 your favourite version of the Google apps @ opengapps.org

The version you will need is ARM64 version 6 for CM13.

Transfer these files to your phone external storage (We will be wiping internal storage).

4. Flash the Cofface edition of TWRP to your Phone either using Fastboot or TWRP.

The reason for this is I have found ZCX version, whilst awesome for seeing and backing up all parts of the MIUI phone, actually breaks non MIUI flashes because it is designed primarily to work well with MIUI Roms (hence we use them to back up)

All TWRP versions can be found here: http://xdaforums.com/redmi-note-3/how-to/guide-redmi-note-3-available-twrps-t3406708/

Once Cofface TWRP is flashed you can move onto step 5 – Flashing Roms.

*NOTE* I have read some people recommend ALKA TWRP to A) backup all partitions, but also B, to flash CM as it does all things. I am only sharing my personal experience of what I have done here, and Alka could work well, but I have not tested it.

All I can say is flashing CM13 with ZCX TWRP Broke my device. – But it was great for making backups.

5. Flashing. Here all you need to do is boot into Cofface TWRP and go to Wipe. Choose advanced options. And wipe ALL partitions you see (Don’t worry, Cofface will not let you wipe out your boot loader, Recovery, IMEI or anything else that is critical) – First flash CM13. Then next, flash the Kate CM13 firmware, and third flash Opengapps. 1 after another (I actually added all three zips in that order and let them flash all together)

6. Reboot and enjoy. You now have an Unrooted CM13 with google apps a working fingerprint reader working radio etc. Happy days.

7. – EMERGENCY FIX EMERGENCY FIX!!! – As I mentioned earlier, TWRP zcx broke my device when I flashed the Roms. I was facing a device decryption error and 0mb data problem.

I fixed this with this URL http://en.miui.com/thread-344450-1-1.html

There is a file there called TWRP_Kenzo_Fix.zip and a batch script that will restore your phone and rebuild the partitions and install Cofface twrp for you!!! So that’s a good option if you break it.

Hope that helps