Is there a way to manually open the hatch from the outside or disengage the locking mechanism entirely so the door will open from the outside? Plot twist: I have a small couch in the back and what are the odds that the actuator stops working the minute I put a couch in there.....

I can't think of way to manually open the tailgate from the outside if it is fully latched or half latched, and the latch motor won't engage. Definitely try removing the negative from the battery and try opening with the latch release button on the tailgate. It is possible to remove the large plastic panel on the inside of the tailgate with the tailgate closed. You will need to remove the bolt connected to the cloth handle and pull out all the clips, then slide it up. With the whole panel and vapor barrier removed you might be able to gain access to the release lever. You need to pull up on the second, smaller lever. With a couch in there that would difficult to do all that, but maybe not completely impossible.

I recently replaced the tailgate window regulator assembly and came across the issue with the door latch not working after putting everything together. Here is a summary of what I learned:

2008 Toyota 4Runner SR5 - Tailgate Repair and Overhaul Summary
2021-01-20

There is a lot going on in the tailgate of 4th generation 4runner. If you live in a winter wonderland it can become a rusty mess in there after a few years.

The space inside the tailgate is known to collect moisture and parts such as the door-latch and power-window regulator assemblies can rust and may fail in damp environments. The latch release button on the tailgate handle is reliable, but the black rubber cover is known to soften/melt in extremely hot weather and might need to be replaced. The latch release button is about $80. You might be able to find just the replacement rubber cover.

On my vehicle, a 2008 4Runner, the right window mount on the power window regulator (rail and cable) assembly rusted and broke-off. The regulator assembly needed to be replaced, while the glass and the power-window motor were removed and re-used. I was able to purchase an OEM rear window regulator assembly via eBay in the USA. The total cost was $250 CAD with shipping and duty and exchange rate ($150 US pre duty/shipping).

All 4th generation 4runners (2003-2009) have the same tailgate and use the same parts as far as I know.
Note that after completing work inside the tailgate, it is a good idea to make sure the tailgate drain holes are open, free of rusty debris or sand, and lubricate everything that looks rusty. A little copper/silver anti-seize on rusty bolts doesn’t hurt.

Most repair work inside the tailgate the involves removing the white connector between the latch and the ECU, typically to open the 5-bolt panel that the ECU in mounted on. It is likely that you will find (after reconnecting this white connector, putting everything together, reinstalling the plastic grey door panel and closing the door) that the door no longer draws in automatically and loosely half latch. The familiar sound of the latching motor is completely absent. At this point you will not be able to open the tailgate, lock your vehicle, or lower the rear window because the tailgate is not closed all the way. No worries. You will need to pop the hood and crawl inside the vehicle.

Reset the ECU:
You likely reconnected everything properly inside the tailgate assembly and you likely did not break a wire, because you were careful. The tailgate ECU does need to be reset. The ECU (electrical control unit) in the tailgate is tied into the vehicle’s overall security locking system. For some reason, if the white connector between the ECU and the latching unit is disconnected and reconnected, even for a few seconds, the door latching motor will no longer operate. To get it working again, disconnect the negative terminal on the battery, wait 30 seconds or so, and reconnect the negative battery terminal. If the door is half-latched, you will need to manually unlatch it from the inside and then push it back in to activate the latching motor. It should automatically draw and operate normally. If not, there could a problem with the latching unit itself, but unlikely if it worked before the overhaul. Despite the cheap feel of the momentary push button on the latching switch, it is more rugged that one might assume. It can be removed and easily tested with a continuity tester on a digital voltmeter. There is also a 10A fuse for the tailgate ECU in the engine compartment fuse called labelled ECU-B. Ensure this is not blown.

Unlatch the tailgate from the inside:
When the door latch motor fails to operate, you will need to manually unlatch the door using the door release lever inside the tailgate. If the tailgate is closed and half-latched, you will need to crawl inside the vehicle to do this.

The manual release for the door latch is accessible on the inside by removing the small grey plastic cover on the door panel. You will likely need to cut a hand-sized hole through the poly-tarp plastic sheet, remove the white plastic box covering the two levers on the left side by pulling up on it. You can reinstall the plastic box and tape up the hole after.

Reach deep into the hole and pull up on the second, smaller lever while pushing gently out on the tailgate. It should release and the door should open. If you have already reset the ECU by disconnecting/reconnecting the negative battery lead you should now be able to push the door closed and the latching motor should operate normally, drawing the door in.
You should now be able to lock and unlock all the doors via the key-fob and the drivers door.

Enable the “rear window down” key-fob button and normalize the rear window:
There is one more issue to address. Since disconnecting the battery negative you will find that you will no longer be able to lower the rear window using the key-fob. The truck will just beep at you. To fix this, insert the key into the ignition, turn it to the ON position, and lower the window using the dash rear window button. You might as well normalize the window at this point, as per the Toyota manual. Normalizing means running the window to its extremes and hold it there for a few seconds.
You should now be able to lower the window with the key-fob “rear window down” button and raise the window by inserting the key into the tailgate keyhole and turning it fully clockwise. Everything should work now, door latch, all locks, wiper, defog, and window up/down. Test them all.

TIP: Remember that you need to press the key-fob doors unlock button twice to unlock all doors including the rear door. A single press unlocks the driver’s door only.

To anyone have the issue where it won’t lock and half opens after a few seconds...this video fixed it for me...watch it carefully and get the little tab in there to move freely, it should follow the lever back when released. Normalization after you reinstal the motor.

https://www.youtube.com/watch?v=VsXnrD7XEls

Thanks for the video was very helpful.

Good video

I went through a similar issue over the weekend. I have 2004 4runner and the rear hatch wouldn't disengage from the lock. You could hear the motor sounds when you tried to open the door but wouldn't work. I bought the latch off Amazon for like $65 bucks. I replaced my old one. I ended up changing it and it seemed to have no power to the new latch. I pulled the blue plug in the rear hatch door for probably 5 minutes then started the 4runner again, then used the defrost, back window and locked/unlocked all the doors and it finally started working like normal. There was def some type of reset for me but I'm unsure what exactly did it.

4th Gen 2007 4runner Sport; intermittent fault where the release button worked, actuator / motor worked but then suddenly nothing. I could hear the motor sometimes run but wouldn't lock or unlock the door. I could only close the hatch to catch on the first lock but couldn't get the door to pull closed like it normally would.
Over a few days and after hours of reading 4th Gen Forums and watching YouTube videos I finally came across this YouTube video which was the exact fix I needed. The video: short, sweet, direct to the point and best of all didn't cost a dime!!!
Hopefully this link to the video will work:
Toyota 4Runner rear hatch repair - YouTube

What did you end up doing? I made a stupid mistake today and may be in the same boat as you were.

https://www.toyota-4runner.org/3785511-post8.html

I have repaired 2 4runners with hatch issues and both were the latch. One of them completely quit and the other was an intermitten problem. Both of them had rust and corrosion on the latch which leads me to believe they are prone to water getting back there.

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