It probably resets with a trip to the dealer for a computer flash.

If it wont go into the PCM or communicate with any modules you have a power/communication problem. The first thing you need to do is find out why the scanner wont communicate. You need to check the power and grounds at the OBDII connector and if they are good check the power and grounds of the PCM. Even if the key module wont read the key the scanner should still connect and communicate so if you diagnose and fix that you should fix the car. I dont remember but do any dash warning lights come on when the key is turned on ? If they do look to see if the "check eng light" comes on when the key is turned on. Many times if it has a PCM problem that "check eng light" wont come on with the key first turned on which it should. It will go out in about 5 to 8 seconds but it should come on when the key is first turned on. Also have you tried to communicate with any other modules ? See if you can communicate with the air bag module or trans module if its an auto. I dont remember what year the Neon got the buss circuit but up to a certain the Neon did not have a buss (communication system between modules) and the PCM communicated over the SCI circuit. For the other modules the DRB III scanner turned on an internal buss to talk with the other modules. Thats why I would see if you can communicate with any of the cars modules. It also may have the SKIM system which is the ign node (SKIM module) or key module as many call it and if it does you should be able to talk to that module with a scanner also. Ron

From what I remember there is no reset on the SKIM system which stands for Sentry Key Immobilizer. You can try unhooking the battery for about 15 minutes as many times that wakes up electronic items. If it is a SKIM problem it would most likely need that module replaced and programed. But you should be able to communicate with the modules on the car with a scanner. Ron

Checking connections isn't enough, at this point you need to access the PCM and check for B+, switched B+ and ground at the PCM.
To do that you will need to be able to connect directly to the harness side terminals-DO NOT PIERCE THE WIRES! Having the proper test leads will also let you check the harness terminals, they can go bad. Then check the wires under a load, most test lights don't provide much of a load. If a circuit fails the test- ie light does not come on, then it's bad, if the light comes on, it MAY be good- there may only be 1 or 2 strands of wire making a connection and not enough to power up the ECM.
I have a headlight that I use to load the circuits and it still let me down on a bus I was working on. In that case the fuse block terminal was going bad and under a prolonged load the terminal would go open circuit. I doubt you have this issue, but there you go.
If you have good power/switched power and ground @ the ECM, well it's time for a new ECM. HTH, Steve

Is it a grey key or black?
Grey is SKIM system / Black is not

The only way I know of to ck and see if the PCM / SKIM module is communicating with the key or not is via the Mopar DRB system.
AKA, a trip to the dealer.

The way a SKIM system works is if the module doesn't recognize the key used to start it, it shuts off. Do this I think 3 times and it no loner allows the key to even turn the engine over.

If when you turn the key on it does not flash the check engine light the PCM is dead most likely

So today we checked the PCM and with the plugs disconnected from it we could get the relays to actuate when the key was turned on and in the crank position it would crank (was using a test light to check for power and noticed it tried to crank when he stabbed that pin, and that the relays were clicking as well). Soooo... Correct me if I'm wrong then this is definitely a bad PCM or does it just need to be reprogrammed?

Yes sounds like bad PCM be warned I once replaced the PCM in 1 of these cars and it ran for 15 minutes {warm up and trip around the block} before it killed the new PCM......the car went to junkyard after that

Jumping in late on this but the first thing you want to do is get it cranking. In doing so you will most likely find why you can't access codes. If The skim theft system was activated it would still allow you to crank and even start and run for 2-3 seconds. Go back to basics(battery,battery terminals ground wire) and find why it won't crank. If you stab a wire and got it to crank you may have a ground issue some where. Somewhere in this diagram is the reason it won't crank;(PCM supplies the starter relay with a ground so if you think it is the PCM then ground that wire and it should crank in the crank position.

Things have been busy and i will look into it this weekend andet you know.

So what fixed it?