Please help me figure out what went wrong...

With the driver's door open, reach around to the rear door inner panel, and manually open the lock knob with your finger. If this is not obvious, look at the driver's door inside panel lock knob and notice you can see orange because the lock knob is in the unlocked position. Move the lock knob of the other door the same way.

Once you can open a rear door, put the rear seat back down and crawl into the hatch area. Then remove the folding hatch floor. The black plastic tray over the spare tire now can be seen. You will find a small rectangular opening at the rear of the tray, facing the hatch lock. Remove the access panel that covers that opening.

Now you will see a shiny metal lever which serves as a mechanical release for the hatch. Move that lever and exert upwards force on the hatch to get it to open.

When you have the hatch open, you can remove the black plastic tray and the triangle hatch floor piece covering the 12V battery.

 

You might be done already, but if still reading, and just in case this is new for you:

With the dead battery, disconnect the negative lead first. And with the new battery, connect the negative lead last.

Also, when the leads are flapping around loose, capping them with a heavy rubber glove (or leather, if that's all you've got) is cheap insurance against something touching what it shouldn't touch.

And before installing the leads on the new post, try to clean out the inside of the clamp. It might be close to pristine anyway, but doesn't hurt. A bit of sandpaper wrapped around a finger, then follow up with a cloth, is good.

Is there a vent tube on gen two? If there's a tube coming off a vent spigot on the dead battery, look for similar vent spigot on the new one.

 

Just to clarify: is the replacement a Toyota supply battery, ie: dimensionally identical to the original battery? Or different/bigger?

Think I know the answer, and if it is bigger, maybe you can put some sort of flexible sleeve over the gap in the ductwork?

Depending on the diameter, maybe some sort of inner tube would work: cutt a longish piece, slip it over both sides of the joint?

 

If your car is a non SKS lock system the OEM battery will be smaller than the Optima. This means that you will need to buy the battery tray for the larger battery fitted to SKS version cars. This is available from your Toyota dealer.

 

I had this happen to me once in a 2008 as well. After getting jumped I was instructed to drive for up to 20-40 minutes on the freeway to get the battery charged up.

Anyways I changed the battery at the full Toyota dealer fee (maybe $500), and it seems it was a good upgrade because it increased my mpg back to 43ish where it was in 2008. I am sure there are cheaper DIY options as well. If its is indeed just the 12v

 

Here's a pretty good walk through:

Prius 12V swap

 

No, you should not be satisfied with this outcome.

1. If the replacement battery is longer than the original, you need to purchase a replacement battery bracket for the Smart-equipped 2G Prius from your local Toyota dealer's parts counter.

2. If the original and replacement battery dimensions are the same, then you need to figure out why the duct does not install correctly. It is possible that you do not have the battery fully seated within the bracket, and that should be fixed so that the battery does not come loose and wobble about, which will shorten its service life.

3. If you really cannot find any reason for the duct not being able to be reinstalled correctly, then it would be better to attach the duct to the inner fender with the provided screw, then use duct tape to secure the other end of the duct to its mate. This will ensure good air flow.

You can find a discussion about the relatively low air volume moved by the traction battery fan, and the need for the rubber panels blocking the duct opening to open up when the car is at speed starting at post #43 here.
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If the duct is not properly connected, you may lose battery ventilation efficiency which will not help the ultimate longevity of the traction battery.

 

You have to pull the rear seats down and crawl into the trunk space and open the rear hatch-sorry to say I forget where the darn latch is.

 

Do as Patrick says and fit the duct work correctly, buying the alternate ducting if needed. You don't want to have saved $100 replacing the 12V battery only to shorten the life of the $2000 traction battery.

For next time: tell your wife that any time she uses accessories in the Prius, just leave the car ON and running, in Park with the parking brake set. Then the battery will not be drained.

 

One way to ascertain what the problem with the ductwork is would be to remove the new battery and try installing the duct with no battery. If it now fits both connections, than you have established that the battery's size or the manner in which it was installed is the cause of the problem. When stuff that fit before doesn't fit now and the only one that has messed with it is YOU, well, I typically don't have to look to far too find the cause of the problem. A mirror can be useful.