Rome Underground - The best places for time travel!

I spent five days in Rome last week. It wasn't my first time in the City - I have visited regularly over college, both for university excavations and for storytelling - but it was the first one in 7 years, and the thought itself made me tear up a little.
(A lot, actually)

There were many new things to discover after 7 years. Of course I visited my ever-favorite places - the Palatine hill in spring bloom, the Etruscan museum in the Villa Giulia, the Ostia Antica archaeological park - but I also got to wander into sites I have not seen before. I especially paid a lot of attention to underground spaces, many of which have been made available to tourists recently, as excavations progress.

I found a very handy little book in one of the museum shops (god, I love museum shops): It is called Subterranean Rome, and it is available in a large-hardcover-fancy edition, as well as a pocketbook format (I got the latter). It lists little known, mostly underground archaeological sites that can take you on a literal walk through different periods in Roman history.
At the end of the 5 days, I did a quick count of how many of these underground, hidden corners of the City I managed to visit (and am happy that I did). Here is the list:

The Roman insula under Santi Giovanni e Paolo
This is the church on the Caelian hill behind the Colosseum. While the church itself, built in the 4th century, is very much worth visiting, the best part can be found under it. A separate little side door leads to a tiny shop where one can buy tickets to see the Roman houses the church has been built over. There are several wall painting preserved, as well as a portion of a Roman street and a house (kind of eerie to walk on a street underground, in dead silence), and my favorite part: a medieval well that has been dug through all this, and now looks like a brick column in the middle of the underground houses. There is also a tiny, but very modern museum underground, with finds from the excavations.
Note: Most churches in Rome are closed between noon and 3pm, or 3:30.

The crypt of Santa Cecilia in Trastevere
We walked into this church kind of by accident, after we found the Aventine rose gardens closed, and we wandered across the bridge into the Trastevere. It is a 5th century church dedicated to the martyr Saint Cecilia. Incidentally we found out the crypts were open for tourists. We wanted to joint a guided tour, but the tiny nun running the church shop sternly told us "NO! CRYPTA!" and ushered us down the stairs on our own.

It was kind of eerie to be down there all alone, but also very beautiful. Next to the Roman era buildings and spaces, there is also the crypt itself, build in neo-byzantine style with fancy columns and mosaics, to worship the saints whose relics are kept in there.
There was also a small side-chamber with shards of Roman pottery from the excavations, and a small lararium with a relief of Minerva in it. It was lit by a separate lamp, and that produced a very nice effect of the goddess' form illuminated while everything else was in shadows.

The Roman temples under San Nicola in Carcere
This church has been built on the Forum Holitorium (the Roman era vegetable and fruit market), next to Marcellus' theater, incorporating three Republic era Roman temples into its walls. It looks fascinating both from the outside and the inside. You can see the Roman columns in the walls, and if you make your way into the underground spaces (after paying 3 Euros per person to a very loquacious information lady), you can see the foundations of the temples, and parts of the Roman walking surfaces. A small tour, but very much worth making.
(In the picture: Roman column in the church wall, and the models of the three temples that got incorporated into the building)

Crypta Balbi
While one of the buildings of the Roman National Museum, it is probably the least visited. Doesn't sport any famous statues or paintings - but it has something much better: Layers. The Crypta Balbi is a building that arches through several centuries, from the Republic all the way to the middle ages, and due to its unique structure, it shows all of them. In addition, the three-story exhibition shows the history of late antiquity and the early middle ages in Rome, illustrating how old buildings decayed and were re-used. It is one of my favorite Roman museums, and it deals with an era that doesn't get a lot of attention, even though it is utterly fascinating. The exhibition includes a lot of models, reconstructions, and illustrations, that make it enjoyable and comprehensive.

Domus Aurea
Definitely the most amazing part of the trip, and a site I have never managed to see before - it is still very much an active archaeological dig, and they only let tourists in (in hard hats and with guides) on the weekends, to raise money for further work. But even the currently excavated portion of Nero's former place is absolutely stunning. It is cavernous in all senses of the word - the size itself is incredible, both in spaces and in the number of rooms already cleared (150+). It has been very well preserved, with many colorful wall paintings and all the structures intact. You can even see the holes in the ceiling where people in the 16th and 17th centuries dug in to take a look at the paintings in torchlight. The palace only stood for about 40 years before Traian had it filled in with soil and buried. It was a waste of a perfectly good palace.
Definitely worth the tickets, unforgettable experience.
Note: You have to reserve tickets in advance to get in; they only do tours on Saturdays and Sundays. I got my tickets here.

Domitian's stadium
The Piazza Navona is always crowded with tourists, but we barely saw any of them descend into the museum to see what the square has been built on - namely, Domitian's stadium for the Capitoline games. The museum is fairly new, and it's very well done; the audio guide is included in the ticket. The space is well-lit and easily walkable; it incorporates the main entrance of the former stadium, well below street level. There were 3 different exhibitions going on when we were there: The history of the stadium itself (with the guide), an exhibit of reconstructions of Roman and Greek helmets and other outfits (e.g. a chariot racer's), and a modern art exhibit using different colored pieces of marble. All of these blended really nicely together, and the museum had a really nice feel to it. I highly recommend it.

Honorable mentions: the San Paolo furi le mura is still one of my favorite Roman churches, and now it has a brand-new underground exhibit of the older structures of the basilica; the Castel Sant'Angelo is much worth visiting, since you can walk straight into Hadrian's tomb; and if you want the real, full, multi-level layer cake experience, don't miss the San Clemente basilica, complete with an underground mithraeum.

Happy travels!