Back to the
map, at the top, you will see "Entrance to Museums"; this is where you enter the Museums. They are called "Museums" because there are in fact multiple museums here, even though they are all part of one complex and are covered by one ticket. You will note that this is a surprisingly long walk (10 or more minutes - it's about a kilometer) for such a small country ;-). You enter at the top, and work you way more or less south through various buildings "Vatican Museums", "Pigna Courtyard", "Apostolic Library", "Belvedere Courtyard", and you end by entering the Sistine Chapel. Once you see the chapel, you exit into an alley next to the Basilica about where the word "Palace" is to the right of the Sistine Chapel. Now you are outside again. Note that this means that it's easy to go from the Museums' exit into the Basilica.
See
for the official webpages on the Museums.
On the northwest side of the City, you see "Old Gardens". Down and to the left, you will see "Lourdes Gardens". These are the areas (I assume both, I've actually never done the garden tour) that are covered by the tour of the gardens. This area is accessible only by prereserved tour.
Info for such tours can be found at
http://mv.vatican.va/3_EN/pages/z-Info/MV_Info_Servizi_Visite.htmlOn the south side of the Basilica is the Ufficio Scavi, or the entrance to the excavations under the Basilica (in fact, under the grotto). This area, rediscovered during World War II, was part of a cemetery next to the circus next to the mons Vaticanus. It is believed that St. Peter was martyred in this circus and buried in this cemetery. The excavations have uncovered a structure where archaeologists believe they have found the bones of the first Pope. If this seems incredible, note that the previous Basilica was built in the 4th Century on the spot where they believed that St. Peter was buried, and even at that time, they had evidence that this was the spot. This story actually has more provenance than many stories coming out of Ancient Rome.
You walk through the excavated area (don't worry, it's fairly tall and you won't feel claustrophobic, even knowing that you are standing under the main altar of the Basilica). You may exit through the Ufficio entrance, or into the grotto (depends on traffic and the whims of your guide).
If you have reservations to the Scavi, then you enter the City at the wooden barricades on the south side of the colonnade, where two Swiss Guards are waiting (where it says "Piazza del Sant'Uffizio"). Tell the guards, "Scavi" (assuming you don't speak any more Italian than that), and they will wave you in the direction of the entrance, which is 100-200 meters ahead, part of the side of the Basilica. As I recall, it says "Ufficio Scavi" over the door.
Note that if you speak German, all the Guards natively speak a form of Swiss-German. In some cases, the Guards themselves don't speak a lot of Italian, although the Italian-speakers are usually the ones doing gate duty both here and at the Porta Sant'Anna on the north side of the colonnade (the employee entrance).
See
http://www.vatican.va/roman_curia/institutions_connected/uffscavi/documents/rc_ic_uffscavi_doc_gen-information_20040112_en.html for info on the Scavi and making reservations (which are required and quite limited).
To access the other areas of the Vatican, you must either be an employee or have a pass to conduct business there (research in the library, errands for the Church, or, in my case, a pass to the bank because I worked for a Catholic University). Look at the travelogue on my Vatican City page for some old photos taken way back then of some of the parts of the Vatican visitors don't get to see.