[Atrix 4G Q&A, Help & Troubleshooting] android-DEP:
No, no need to order a battery, there's nothing wrong with your current battery.

This was exactly the same way I first soft-bricked my first atrix long long ago. The battery would not charge no matter what I did and I could not flash anything onto the phone because the charge was too low and kept getting lower. It eventually fell to the point where it was like less than 5% charge left on the phone.

For some stupid reason, the Atrix does not recharge the battery when you do not have a proper working installation currently on the phone, like a corrupt install where something didn't do what it was supposed to do.

The catch is that once this happens and you have a corrupt install of whatever rom half-ass installed that doesn't boot, perhaps maybe even if the rom improperly wiped out the recovery so you can't boot into recovery, the phone will not recharge itself anymore. This is one MAJOR reason why you should always flash your phone with a FULL battery charge, not because it's cool to have a full battery icon on the statusbar, but when the fit hits the shan and things go wrong, you have some spare life left to be able to to try flashing something else to recovery your phone with before it drains too low.

You have 2 options at this point, you basically have to find a full charged up battery to use for about 10 minutes. Reason I say you have to find a battery and not just say find someone with an Atrix is because you can also use the battery from the Motorola Droid.

This was what I did once I finally found someone near by with a Droid, I borrowed their battery for 10 minutes to restore my phone and it worked like a charm.

Atrix battery model is BH6X and the Droid battery is BH5X which is the same size but has a weaker mAh. Long term I dont know how safe it is to continually use that battery but for something like restoring your phone, using that battery is perfectly ok unless you have a friend who has an Atrix also. Have him charge his battery up to full and then swap batteries with him so he can continue charging while being able to use his phone and you will have a full charge which buys you enough time to recover your phone before you drain the battery from flashing.

This was the exact reason I purchased this charger & battery just in case of just in case

Only thing is that this generic battery is 1800mAh 6.7Wh and the factory battery is 1880mAh 7.0/7.1 Wh but I never had any issues with the generic battery.

You can optionally get this nice Dual Dock Cradle + 3 batteries

Here's another option, 2000mAh battery with external charger

The way I solved my issue was to download a fresh copy of a 2.3.4 SBF file and a good copy of RSD Lite. Once I popped in the battery into my phone, I hooked it up to RSD Lite and just let it do it's job to restore everything back to square 1. Locked bootloader, not rooted, deodexed or zipaligned. But back then these things didn't matter as long as I was able to recover my phone and not have to pay $125 to send it to AT&T insurance dept. just to get a refurbished one in exchange.

I truly believe this is one situation which does earn the necessary required use of an SBF file to be flashed with RSD Lite. There's risks involved with flashing SBF files and so it's best to avoid them altogether but there are only a handful of certain situations which do call for their use such as recovering\restoring your device from an unusable state.

Definitely do some more reading about the matter and what your options are here. You're going to have to keep an eye out for the pros vs. the cons of using certain methods to recover a soft bricked phone. I'm sure last thing you want your phone to be is a hat weight right? lol, but do yourself a favor and read up more about this before you decide your course of action. Don't just start flashing anything that pops up that seems like it will work ;)