I am going to create a game console. The games will be in an SD card and an Arduino (or an Atmega chip) will read a hex file's contents to RAM and will flash it to another one. Something like this but here, the guy says that this only works for atmega328, and I am planning to use a ATSAM3X8E chip and also I am worried about the power levels (5v - 3v3).
Is there any way for me to use an Atmega chip like Atmega16u2 and use that to flash something like an ATSAM3X8E? If so, what protocol should I use and how may I implement it in my code?