To enable the JTAG Interface on an Arduino Mega the JTAGEN fuse bit must be set to zero.

A modified Arduino bootloader with JTAGEN fuse bit enabled can be programmed by using an Arduino Uno as ISP (In-circuit Serial Programmer).

The Arduino IDE can be used to burn the bootloader after making the following modifications to <Arduino IDE Path>\hardware\arduino\avr\boards.txt

"C:\Program Files (x86)\Arduino\hardware\arduino\avr\boards.txt"

The following calculator can be useful to calculate the correct value: Fusecalc

The mega.menu.cpu.atmega2560.bootloader.high_fuses value is modified from 0xD8 to 0x98

## Arduino Mega w/ ATmega2560
## -------------------------
mega.menu.cpu.atmega2560=ATmega2560 (Mega 2560)

mega.menu.cpu.atmega2560.upload.protocol=wiring
mega.menu.cpu.atmega2560.upload.maximum_size=253952
mega.menu.cpu.atmega2560.upload.speed=115200

# mega.menu.cpu.atmega2560.bootloader.high_fuses=0xD8
mega.menu.cpu.atmega2560.bootloader.high_fuses=0x98

Connect the Arduino ISP (Arduino Uno) to the target (Arduino Mega).
Connect the Arduino ISP (Arduino Uno) to the PC with an USB cable.

Arduino Uno (Pin)	Arduino Mega ICSP Header (Pin)
5V	5V
GND	GND
10	RESET
11	MOSI
12	MISO
13	SCK

More information about creating an Arduino ISP (In-circuit Serial Programmer): Tutorial ArduinoISP

When board, processor and port is setup correctly and the programmer is connected to the target the Bootloader can be burned from the Arduino IDE.

After burning the bootloader the JTAGEN fuse should be enabled.

Additionally, clear the JTD bit in the MCUCR register.
This can be done by creating a new Arduino Mega (ATmega2560) project with Visual Studio Code using the PlatformIO IDE extension.

The following code will clear the JTD bit without changing the other bits in the MCUCR register:

void setup() {
// put your setup code here, to run once:
MCUCR = MCUCR & ~(1<<JTD);
}

void loop() {
// put your main code here, to run repeatedly:
}

Pins A4-A7 are now configured as JTAG signals: TCK, TMS, TDO, TDI.

 

Please read the following disclaimer before making changes to your device / software:

Disclaimer

* I'm not responsible for bricked devices, dead SD cards, thermonuclear war, or you getting fired because the alarm app failed.
* YOU are choosing to make these modifications, and if you point the finger at me for messing up your device, I will laugh at you.
* Your warranty will be void if you tamper with any part of your device / software.