You need a bunker then set your employees to 'research' so they work to unlock the mk2 weqpons. Pay or steal supplies and let your workers use the supplies for the research. If you want research to build up faster, you can call Agent 14 to do a steal mission for research to boost research bar by 33%, or once you have one notch in research, you can login to bunker computer and pay for the remaining bar of research.

Then once you've got the mk2 weapons unlocked via research, you need a Terrorbyte or MOC (maybe Avenger too buy I don't have one so not sure), with the weapons workshop equipped in the vehicle, then you can pay to convert your existing weapons to Mk2 weapons.

It's expensive and takes a lot of time.