Diesel will crank over but will not start

I am not sure I understand the issue.

The vehicle will not start unless you connect the scan tool to the DLC? However, the DLC will not connect to the vehicle?

Is it possible to get a video of this? Basically get a video of trying to start the engine and then connect the scan tool and start the engine?

I am not doubting that this is what is happening, I am just hoping that seeing this will point to an issue because connecting to the DLC has absolutely nothing to do with starting the engine.

Also, you selected this was a 1999 Ford Transit we don't have a manual on this vehicle as it was not offered in the USA until 2010 but if this is a Diesel engine, then the principals are the same to start the engine.

https://www.2carpros.com/articles/car-cranks-but-wont-start

What I would suggest starting with is using ether in the intake and see if the engine starts and stalls.

If it does then we have a fuel issue. If not then we need to check and make sure the theft system is not active.

The only thing I can think of that would be related to a scan tool being connected and the vehicle starting would be the theft system. Again this would not be directly related but seeing it I think will help get us on the same page.

Thanks