You need to make sure that you can flash the arduino bootloader again onto the chip.

For this you need an programmer like the AVR Dragon.

This is the wiring connection for the AVR Dragon to the Trigorilla ISP connector:

To flash the bootloader, download and install avrdude:

• http://download.savannah.gnu.org/releases/avrdude/
• http://download.savannah.gnu.org/releases/avrdude/avrdude-6.3.tar.gz

• http://www.nongnu.org/avrdude/user-manual/avrdude_18.html#Unix

gunzip -c avrdude-6.3.tar.gz | tar xf -
cd avrdude-6.0
./configure
make
su root -c 'make install'

In /etc/udev/rules.d add (obviously as root user) the following file: 45-atmel.rules

# Atmel Corp. Dragon
ATTR{idVendor}=="03eb", ATTR{idProduct}=="2107", MODE="660", GROUP="dialout"

Then reload udev rules with:

sudo udevadm control --reload-rules && udevadm trigger

Steps and information below basically follow the description from here and here.

A bootloader can be found in the arduino directory from where you downloaded the arduino IDE itself. The location for Arduino-1.8.5 is:

Original bootloader:

arduino-1.8.5/hardware/arduino/avr/bootloaders/stk500v2/Mega2560-prod-firmware-2011-06-29.hex

or the newer one that fixes the WDT and the !!! problems¹⁾:

arduino-1.8.5/hardware/arduino/avr/bootloaders/stk500v2/stk500boot_v2_mega2560.hex

avrdude -p m2560 -P usb -c dragon_isp -v

avrdude -p m2560 -c dragon_isp -P usb -Ulock:w:0x3F:m -Uefuse:w:0xFD:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m -e -v

To prevent an error with the fuse setting at the verification step²⁾, change this command in:

avrdude -p m2560 -c dragon_isp -P usb -Ulock:w:0xFF:m -Uefuse:w:0xFD:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m -e -v

avrdude -p m2560 -c dragon_isp -P usb -Uflash:w:stk500boot_v2_mega2560.hex:i -Ulock:w:0x0f:m -v

Similarly, to prevent an error with the fuse setting at the verification step³⁾, change this command in:

avrdude -p m2560 -c dragon_isp -P usb -Uflash:w:stk500boot_v2_mega2560.hex:i -Ulock:w:0xcf:m -v

If you get an error like the following with avrdude:

...
Reading | ################################################## | 100% 0.05s
 
avrdude: verifying ...
avrdude: verification error, first mismatch at byte 0x0000
         0xcf != 0x0f
avrdude: verification error; content mismatch
...

You may have to change the fuse setting verification step⁴⁾. See above for the change.

• https://learn.sparkfun.com/tutorials/installing-an-arduino-bootloader/all