a day in stockholm

I appreciate your effort to make the best of less than ideal travel arrangements. 12 1/2 hours is a long time to be stuck in an airport, especially when that airport is located on the edge of a truly wonderful city.
The task at hand is clearly time management.
Can you store your luggage at Arlanda airport? Yes. Can you go sightseeing for the day? Yes.
Arlanda is located 30 minutes from central station in Stockholm by train.
Airport to central station and back takes one hour of your sightseeing plus wait time for the trains.
Directly across the street from the central station (on the north side of the street) is a pick up point for several "hop-on hop-off" buses (one even includes boats). You could ride around and see the city - getting on and off as you choose.
Or, you could familiarize yourself with the area near the station and pick two "must see" attractions (there are many in the area).
I like the out door museum (Skansen) and the Nordic museum - that's where I would go.
Keep your eye on the time......it will fly by (so will your connecting flight - hopefully, with you on it.)

Yes, take the Arlanda Express from the airport. For the two top attractions visit VASA Museum and Drottingholm Palace where the royals live. Take a boat there. Enjoy the gardens.
Walk around Gamla Stan, old town. The City Hall offers a very interesting tour. These are not far apart.
I was there for about a week and don’t recall seeing hop on hop off. We used transit pases bit mostly walked and took the little ferries( coverd by transit pass.)

If this is your first time in Stockholm, I suggest avoiding the museums and enjoy Gamla Stan and the waterfront. Relax, get some sun before your next flight. If you get bored, ride a ferry or walk over to Sodermalm and walk Monteliusvägen. It's a beautiful city so mostly stay outside.

Make sure you take the Arlanda Express high speed train.
I would go to Vasa Museum and spend the rest of the time at Gamla Stan.

Thank you all will do as suggested...will checkout the high speed train & walk out old town.

Agree with Wray and vandrabrud. It’s about a 15 -20 min walk to Gamla Stan. Probably double that to Skansen or the Vasa, so a bus might be wise. Just map it out well before you get there.