2004 BMW X3
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We took the back hatch off and when we put it back on the vehicle will roll over but will not start, what should we do or where should we start?

There is nothing in the rear hatch area that would do what you claim unless there is a ground wire that was forgotten or perhaps a preexisting condition. A crank, no start condition will set a fault and it is readable with proprietary software. Will it start if you spray carburetor cleaner into the intake? If so then fuel delivery is an issue, start with checking the fuel pressure and delivery. BTW, just to satisfy curiosity, what did the hatch come off the car for?

I was wrong the back hatch was not taken off. this is what happend. the battery was dead and the son put the battery charger on it, but put them on backwards. while it was hooked up he pushed the button to pop the back hatch. then after that we found out what happend and put a new battery in. the car would start and run but the back hatch would not work. so, they torn the back hatch apart and check for power with a test light and then it would never run after that. we do have a fuel smell out the exhaust and tried to put ether in it and it will still not run, but it will roll over. so something is wrong with the relay to the back hatch and we do not know where to find that b/c we have replaced the actualor on the back hatch latch and the new swith to the latch and the hatch still does not work and the car wont start. everything else works and we do not have the software for 2004 x3 and we cant buy a manual b/c no one can get them for the x3. what should we do or where should we look?

You will need to go to the dealer for repairs. Reversing the battery voltage is very, very bad and you have most likely caused severe damage to the engine control module.

would that have to do with the back hatch not working too? also where would the reley be for the back hatch? thanks

The general module controls the central locking, the sunroof, and the rear hatch. There is no separate relay. What this has to do with it is that the X3 platform is very sensitive as far as the electronic modules go and reversing the charge at the battery may have caused damage to several modules and you will need to go to the dealer to repair these issues. As the little sticker on some electronic devices says "there are no user serviceable parts inside" I am sorry if this advice seems harsh, but there is a price to pay for not following the correct procedures and letting unqualified personnel perform repairs on your vehicle.

would there be a fusable link somewhere to this, b/c the car did run after he crossed the terminals it is when they used the check light that the vehicle would not run anymore.

A light used to test circuitry might not cause this but there is a possibility there is an issue with some of the electronics. First let's try the easy stuff, disconnect the battery for 10 minutes, this is what BMW calls a master battery reset, its like control, alt, delete on your computer, then reconnect the battery and try it again.