Unfortunately the museum on Hoy is closed at the moment for remodelling and will remain so until sometime next year. Apparently some exhibits are on display at the Hoy Hotel - which looks like this:
I'm just back from Orkney where I spent a long weekend. I didn't bother taking the ferry over to Hoy to chance the hotel.
Instead I went up to Birsay and enjoyed very fine weather and atypically warm seawater!
Heading a couple of miles out of Kirkwall to Scapa itself, there is a memorial to HMS Royal Oak. The wreck marker is visible from the shore (and dead centre in the photograph below). I didn't take photographs inside the memorial building - it felt crass and disrespectful to even contemplate it when I was standing in there.
The Churchill Barriers are of course worth a look as are the associated block ships
There's a small but good museum, but it is over on Hoy, and a number of surviving hardstandings/buildings will also require a ferry ride. I'm sure any local taxidriver will help. There's also the Churchill barriers which are easy to get to.
Personally however, once you've seen the Flow itself, the prehistoric sites will be much more impressive. The ship's visit will be all too short.
We're halfway through a wonderful 15-day cruise of the British Isles and tomorrow will arrive in Kirkwall, in the Orkney Islands. Hoping to get to spend some time seeing what was once the famous naval base of Scapa Flow, which I've wanted to visit for many years.
Loved seeing the fantastic Belfast Titanic museum, including SS Nomadic, the ship's restored lighter.