The Doctor V64 was a 3rd Party Development kit and Piracy device that was much cheaper than the official nintendo development kits 1. It is the original Creator of .v64 files (it has functionality to dump carts) and even came with a CD full of N64 roms.
The Bung Dr V64 required a cartridge to be placed in the cartridge slot in order to interrupt the signal coming from the official game cartridge and instead send the data from the V64. The original cartridge that you put in the top was just used for the CIC anti-piracy check.
Doctor V64 emulation cartridge adapter; 50-pin connector and PCB with solder across pin 9 and 10 #N64dev pic.twitter.com/tqrdJB9wZU— Shane Battye 🎮 (@shanebattye) January 30, 2018