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

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

avrdude -p m2560 -c dragon_isp -P usb -Uflash:w:stk500boot_v2_mega2560.hex:i -Ulock:w:0x0f:m -v
 
avrdude: Version 6.3, compiled on Mar 11 2020 at 23:44:01
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2014 Joerg Wunsch
 
         System wide configuration file is "/usr/local/etc/avrdude.conf"
         User configuration file is "/home/mni/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping
 
         Using Port                    : usb
         Using Programmer              : dragon_isp
avrdude: usbdev_open(): Found AVRDRAGON, serno: 00A200007476
JTAG ICE mkII sign-on message:
Communications protocol version: 1
M_MCU:
  boot-loader FW version:        255
  firmware version:              7.33
  hardware version:              1
S_MCU:
  boot-loader FW version:        255
  firmware version:              7.33
  hardware version:              7
Serial number:                   00:a2:00:00:74:76
Device ID:                       AVRDRAGON
         AVR Part                      : ATmega2560
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :
 
                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    10     8    0 no       4096    8      0  9000  9000 0x00 0x00
           flash         65    10   256    0 yes    262144  256   1024  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00
 
         Programmer Type : DRAGON_ISP
         Description     : Atmel AVR Dragon in ISP mode
         Vtarget         : 4.9 V
         SCK period      : 4.00 us
 
avrdude: AVR device initialized and ready to accept instructions
 
Reading | ################################################## | 100% 0.15s
 
avrdude: Device signature = 0x1e9801 (probably m2560)
avrdude: safemode: hfuse reads as D8
avrdude: safemode: efuse reads as FD
avrdude: NOTE: "flash" memory has been specified, an erase cycle will be performed
         To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "stk500boot_v2_mega2560.hex"
avrdude: writing flash (261406 bytes):
 
Writing | ################################################## | 100% 0.00s
 
avrdude: 261406 bytes of flash written
avrdude: verifying flash memory against stk500boot_v2_mega2560.hex:
avrdude: load data flash data from input file stk500boot_v2_mega2560.hex:
avrdude: input file stk500boot_v2_mega2560.hex contains 261406 bytes
avrdude: reading on-chip flash data:
 
Reading | ################################################## | 100% 0.00s
 
avrdude: verifying ...
avrdude: 261406 bytes of flash verified
avrdude: reading input file "0x0f"
avrdude: writing lock (1 bytes):
 
Writing | ################################################## | 100% 0.06s
 
avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x0f:
avrdude: load data lock data from input file 0x0f:
avrdude: input file 0x0f contains 1 bytes
avrdude: reading on-chip lock data:
 
Reading | ################################################## | 100% 0.05s
 
avrdude: verifying ...
avrdude: verification error, first mismatch at byte 0x0000
         0xcf != 0x0f
avrdude: verification error; content mismatch
 
avrdude: safemode: hfuse reads as D8
avrdude: safemode: efuse reads as FD
avrdude: safemode: Fuses OK (E:FD, H:D8, L:FF)
 
avrdude done.  Thank you.

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