Okay, as a native of the Boston area, I will graciously help Ruby out with things that you can still do in Boston. As stated, you have museums like the MFA (Green, E line - MFA stop), the Harvard Museum of Natural History and their various art/ethnic museums that you get in (Red Line, Harvard Stop), the Isabella Stewart Gardner museum (very walkable from MFA, but Green, E Line, Longwood Medical Area is technically the closest stop), if you like contemporary art, there is the ICA near South Station, Red Line, plus a whole host of small modern art pop ups across the metro Boston area. Further out, I really enjoyed the Peabody Essex museum (closest stop is Salem on the Commuter Rail Newburyport Line).
Like gothic architecture? Then hit up the Boston Public Library at Copley Square (Green Line, any line, Copley), and go through the main entrance and enjoy the dark academic vibes and massive murals made by John Singer Sargent who I'm sure Ruby totally knows about.
Then enjoy walking by (maybe into?) Trinity Church across the square and head up Newbury/Marlborough Street and enjoy the Back Bay architecture and all the cute little (expensive) stores. If you time it right, one of the churches might be offering a free, or very cheap concert, and those spaces are always beautiful. If you can extend this, you could walk into Beacon Hill and find all the hidden stores and parks there. I always find something new there. Then you can enter the Massachusetts State House (both old and new), it's great to explore there. And of course, Harvard. They have the cutest (pricey) damn dorm houses too when near the school. Looks like little cottages. If you go West of Harvard, you also get to enjoy those classic brick streets, and peep into some parks up there. Counter to what some posters said, it's actually pretty easy to get into Harvard buildings, and Ruby could likely easily enter some common spaces in Harvard/MIT/BC/NEU. Or you could just stand outside one and hope someone mistakes you for a student and lets you in, heh.
I will take this paragraph to plug in a few more local bookshops: the Commonwealth Bookshop right down the alley from State Street Station (Orange Line), the Brookline Booksmith, Harvard/MIT COOPs, Raven Used Book, Bryn Mawr Book Store, the Anarachist Bookstore (a bookstore run on anarachist principles), etc etc etc Boston have an AMAZING selection of small, independent bookstores.
If you like urban nature, I cannot stress enough to visit the Emerald Necklace parks made by famous landscape architect Fredrick Law Olmsted (the creator of Central Park in NYC). These follow the Muddy River and if you have the energy to walk 15 miles (I did do this once), almost all of them can be walked. If not, they are along the Green Line, primarily D and E, stops. And yes, the Green Line was named for the Emerald Necklace. This covers the Muddy River, Ward, Willow, and Leverett Ponds, and the huge Jamaica Pond. The last bits are the Arnold Arboretum (Orange Line, Forest Hills), and Franklin Park which you'd need to bus or take an uber to, but I highly recommend if not for the abandoned, early 20th century bear cages. Then you have Harvard Yahd, the Boston Boardwalks, the Boston Islands are really nice, but might be chilly at this time. Will shout out the popular George's Island for its Civil War fort (that was really more of a military prison) that you can explore.
Boston also have a rich history of the Black, Abolitionist movement, Japanese cultural exchange, among others, but Ruby probably doesn't care about that.
Honestly, it's really baffling that Ruby hasn't hit on anything else. Like at this point it's more a matter of looking at your environment than having to go anywhere. Like Ruby has to have her eyes down, on her phone, the entire time to miss all this especially since stuff like Back Bay and Beacon Hill are stone's throw from where she is staying.