This is a simple guide to debricking a Kindle 3 using Freescale's Advanced Tool Kit. If you feel like you need to edit this to include details, go right ahead.
I really, really advocate using Kubrick instead of ATK. Kubrick works better, has a higher success rate, is less complicated, and easier to support, from a developer standpoint. If you really must use ATK, then proceed, at your own risk. --qlob
Freescale ATK not available for download using the below link as of 22/09/2018 rendering instructions unusable.
 Before you do anything, let your Kindle charge for 2 or 3 days.
- there are also hardware difficulties that can seem like a bricked kindle, be sure to check for dislodged ribbon cable on the lower left side of the opened kindle. if this cable becomes unconnected, the screen will appear to freeze and cease updating. (image to come if I can find a way)
- Don't panic. This has been proven to work (unless you happen to have a hardware failure)
- Download both images from the Debricking thread on the first page of the MobileRead Kindle Developer's Corner forum. Make sure that the images you download are specifically for the Kindle 3. Use the 3.0.2 kernel and mmcblk0p1 files from the "simple debricking" pastebin page. Be sure to download both parts of mmcblk0p1 before unzipping it. Do not worry about the differences between the Kindle 3 wifi only and the Kindle 3 wifi + 3g as the images will work for both. They should be sized around: Kernel Image:~3 MB and Root Filesystem Image: ~650 MB. After you download the files, decompress them until you reach the .img extension (the mmcblk0p1 is compressed twice). Then, rename the smaller one to kernel.bin and the larger one to rootfs.bin.
- Download and install Freescale Advanced Toolkit (commonly referred to as ATK in this guide and online). This only works for Windows, but a Linux tool is being developed as you read this. NOTE: When installing on a Windows 64bit system it is possible that the USB drivers needed for this process will not install. The easiest option is to utilize a Windows 32bit system instead. If you try performing step 4 below and you get a "No USB detected" popup box after hitting next, this is the sign that the drivers did not install.
- Connect your Kindle via USB to the computer. Hold the power button for 30 seconds and then without letting go, press and hold the vol - button for 1 second, then release only the power button, wait 1 second, then release the volume button.
- Run ATK. A window should pop up with several sections. The first one you should worry about is the CPU section. In the dropdown menu change the value to iMX35_T02. The next dropdown menu needs to be changed to mDDR. After that, select the button that says USB. then click next.
- Now, two buttons should appear. Select the Flash Tool button and click Go at the bottom.
- In the upper left hand corner, click program.
- In the center, browse to where you saved kernel.bin and select it.
- In the dropdown menu in the upper right, select MMC/SD.
- Enter 00041000 in the first box of the operation settings section.
- At the bottom click Program.
- In the center, click browse and select rootfs.bin.
- Enter 003C1000 in the address box of the operation settings.
- Click Program.
- Wait. (Take your time. Since the filesystem image is around 600 to 750 MB, this can take up to 4 hours)
- Unplug and reboot your Kindle.
- If your Kindle boots successfully, connect it to the computer again. If you see random gibberish on the computer you will have to make a new VFAT filesystem on the Kindle.
The original version of this guide was written on a Kindle (using KindleNote) that has been debricked thrice using this method.