It's difficult to tell exactly what is going on from the photos. Is your foundation wood? My best advice is to that a licensed general contractor come view the atrium and let him/her offer their advice on how to repair and how to prevent future damage.

You can repair, but it will happen again over the next several years, if you don't have any drainage. You need to excavate and add some type of a drain that flows to the outside area.

You need proper drainage and that will require some excavation and a way to get the water out of the atrium. We had one in Vancouver but it was built into the home constarction at the build stage adding it now will be tricky . It looks like you have wood that is od for this type of structure so it will require a lot of work best done by someone who understands the issue . The pictures are not helpful since I can't even make out what they are showing

Just back yer ears and start ripping out until you reach undamaged wood then build it back. May as well post other issue if you have any, that way we can walk you through them all while your tools are laid out.

I will post a video that shows the problem better

Good idea, after viewing your video someone here can post a video showing how to fix it. Will you need a tool list as well ?

How big is the opening in the roof? Could you add a skylight/s to enclose it?

Yes to the tool list. The opening is 4’ft x 12 ft approximately

The forum doesn’t enable videos to post - I think you need a pro on site to help you think through adding drainage

Here is a video of the area that needs repair. I have a flat roof . The rain came quickly and leaked through the roof and it covered the entire living room. The area that leaked came from the roof and down through the ceiling. To help the problem I had a new flat room put on.that slants away from the atrium. We need to know how to fix the section with the rotted wood before new windows are installed. The current windows are single pane and have not been resealed since the late 70s

Here are pictures since the video will not post

Here is the area

Where the corner is

Another. View

The first thing to do is to reduce the water coming in. Does the roof funnel water away from the atrium? Then, what's the soil? Clay, sand, in between.

Removing dirt won't help with the drainage, unless there's clay under there and you remove enough to provide room for any water. That said, if you dig a pit in slow-draining clay and it gets filled with water, it won't be good, even if you've put something like sand or better soil in the pit.

You might find inspiration in knowing when you complete this project you will be fully qualified to build a room onto a home or build a modest single story home from ground up.

I believe it. What tools do you use we need?

I had the flat roof replaced and instructed the roofers to direct the water away from the atrium towards the drain . We are intdrain.

We are also digging in the atrium. There is a lot of stones on top and will see what is underneath. That’s for the info

The problem is how do we repair the wood that is damaged and not destroy the window frame

I am talking to a friend who is a civil engineer to get some advice

From what I see you have a slab on grade. The rotted wood is your wall sill plate sitting on that slab.

The roof leak during that rain event allowed you notice the rotted sill, but that problem occurred more likely through capillary action rising up behind the stucco over many years, and possibly from the wood not being treated nor having a sill gasket, as your rot is not from a single incident, the wood is continuously damp.

To prevent this rot and pests in the future, and why code requires it, grade (and that should include the rock landscaping) should be no higher than 6" to the bottom of wood (the sill plate or any wood sheathing behind stucco). That means you would see the side of the concrete slab exposed (or in your case the stucco finish probably stops somewhere along that slab edge, and probably not in a crisp clean line).

So continue digging out the atrium, and if you do not have an area that a pipe can exit to the outside yard, then you will have to install a drywell. That would be a below-grade "pit" that water runs to and is stored, where it slowly dissipates into the surrounding dry soil. It can be a large stone pit, covered or not, a plastic perforated crock, or it can even be just a deep pipe. The atrium floor should slope towards this drywell, and in crock/pipe versions would have a floor drain.

There are some details to know about in whichever version you choose, and for the replacement portions of wood sill it sounds like that might be beyond your wheelhouse. So a contractor should be able to replace the sill and patch the stucco while they are replacing windows (those might require stucco repair anyway).