[One (M9) Q&A, Help & Troubleshooting] CryloRends:
Alright guys, I'm new to posting here but I used tutorials from here to root my LG G-Flex 2 and now my HTC One M9. I rooted it about 4 months ago, used it normally for a portion of that, for a time the charger port was broken so I had to get that fixed and got it back still normal, rooted and with TWRP as a custom recovery and such but otherwise working perfectly fine.

I had the android update notification up in my face all the time and I couldn't get rid of it myself and couldn't be bothered wasting too much time fixing it so I just decided I'd unroot the phone and go back to normal android since I hardly took advantage of the fact that it was rooted anyway.. I downloaded the system update and told it to install, I figured this would just get rid of the root for me and all would be good, but it didn't work. It would start the update then just boot itself into TWRP as normal. TWRP was getting in the way of it going into normal recovery mode to do the update.

This is where I ****ed up big time, and I know this was entirely my fault and I feel retarded for thinking it would do anything other than what it did. I went into the Wipe option in TWRP (V2.8.5.0 btw) and wiped the entire system folder. I don't know what I was thinking, something in my head made me think it would just factory reset the system and get rid of the root, which was just dumb as hell because it wouldn't have changed the custom recovery or anything anyway, and it didn't..

I've tried everything I can think of, the phone boots into all the different modes normally, Bootloader works fine, Download mode works fine, recovery works fine.

I used Squabbi's HTC One M9 Toolkit V 1.6.1.0 to update my TWRP to 3.0.0 but it won't go any higher than that without just looping until I flash it back to 3.0.0. I have tried ADB sideloading, it won't work, adb won't even read the Viper zip file I have in the same folder and stuff correctly. I've tried using an SD card to put the Viper zip onto the phones internal storage and install using TWRP, it all installs correctly and encounters zero problems but when I reboot the phone it just boots to the bootloader, the same thing happens when I tried Android Revolution ROM.

adb push command doesn't do anything, adb sideload doesn't do anything, nothing does anything.

I should also mention my HTC One M9 should be the international model, I live in Australia, its second hand and works with 2 different carriers that I have tried it with, I'm with Optus and didn't have to get it unlocked to use my SIM with it right away.

For transparancy I'll list out what is shown on each screen in case it helps in some way..

In download mode:

hTC download mode

*** UNLOCKED ***

htc_himauhl PVT S-ON

LK-1.0.0.0000

RADIO-01.04_U11440601_71.02.50709G_F

OpenDSP-v29.2.6-00492-M8994_0702

OS-2.9.710.5

Sep 30 2015, 14:12:12(573756)

system info

show barcode

reboot to bootloader

reboot to download mode

reboot

power down

^ Those all function properly except for reboot, that reboots to bootloader.

In bootloader:

*** Software status: Modified ***

*** Unlocked ***

*** S-ON ***

and all the menu items as normal, again all function properly except for the general reboot.

The phone has been completely system wiped with TWRP now, flashing new ROMs still doesn't work.

I'd like it if people could give me suggestions and I can let you know if I've tried them already since I have tried a fairly large array of things to fix this problem, some of them I can't remember right now tbh..

Thanks all :)

UPDATE: Using lamahgra's suggestion I have successfully fixed the problem, phone is functioning perfectly normally now :)