Secret locations

Secret Locations were memories that involved a combination of freerunning and puzzle solving. Many of these locations were scattered throughout Italy and Constantinople, and were explored by the Assassin Ezio Auditore da Firenze during the Renaissance.

The locations were mainly an optional element, with the exception of the Assassin Tomb inside the Santa Maria Novella, the Lair of Romulus inside the Terme di Traiano, and the four locations traversed in order to collect the Masyaf Keys. However, they offered various additional benefits once they had been fully explored, such as the armor and weapons of key Assassin and Templar figures, or a substantial sum of money.

Assassin Tombs
The Assassin Tombs were seven landmarks around Italy, each containing the tomb of an Assassin who was said to have "protected the freedom of mankind when it was most threatened". They also contained an Assassin seal (with the exception of Domenico Auditore's tomb), which were collectively used to obtain the Armor of Altaïr within the sanctuary beneath the Villa Auditore.
 * Santa Maria Novella - contained the tomb of Darius.
 * Il Duomo - contained the tomb of Iltani.
 * Auditore Family Crypt - contained the tomb of Domenico Auditore and his son.
 * Torre Grossa - contained the tomb of Wei Yu.
 * Rocca di Ravaldino - contained the tomb of Qulan Gal.
 * Basilica di San Marco - contained the tomb of Amunet.
 * Santa Maria della Visitazione - contained the tomb of Leonius.

Templar Lairs
The Templar Lairs hid treasure that presumably belonged to and funded the activities of the Templar Order (with the exception of the Palazzo Medici). All of these could be accessed through a wooden door marked with a large red cross.
 * Palazzo Medici in Florence.
 * Santa Maria Dei Frari in Venice.
 * Arsenal Shipyard in Venice.

Rome
Secret locations were also found in Rome, in the form of Lairs of Romulus. There were six of them in total, located throughout the city at various landmarks. Additionally, there were also two Templar Lairs that could be found in Rome.

Completing all of the Lairs of the Followers of Romulus would allow Ezio to obtain two of the treasures they guarded, which were the armor and dagger of Brutus. Through traversing these locations, Ezio also obtained documents that gave background details on the cult, as well as the Assassin Marcus Junius Brutus, a Roman senator during the time of Gaius Julius Caesar.

Lairs of Romulus

 * Catacombe di Roma.
 * Terme di Traiano.
 * Colosseo.
 * Cloaca Maxima.
 * Palazzo Laterano.
 * Basilica di San Pietro.

Templar Lairs

 * Aqueducts.
 * Mercati di Traiano.

Constantinople
In Constantinople, there were many secret locations that could be explored.

Masyaf Keys
As the main focus for Ezio Auditore's search for knowledge, he sought out the locations of the keys to the library of Altaïr Ibn-La'Ahad. A map to each location could be found in rare books, which were hidden within the city of Constantinople.
 * Yerebatan Cistern.
 * Galata Tower.
 * Forum of the Ox.
 * Maiden's Tower.

Others
As well as locations that hid the Keys, two other secret locations resided in the city.
 * Hagia Sophia - required Ishak Pasha's memoirs to be found.
 * Vlad the Impaler's Prison - available from a tome in Sofia Sartor's book shop.

Pegleg trinkets
Collecting trinkets for a man nicknamed "Pegleg" allowed Ratonhnhaké:ton to explore secret locations in the search of William Kidd's hidden treasure. These locations were unlocked after giving the trinkets to Pegleg, to which the Assassin could access these locations by interacting with Robert Faulkner.
 * Fort Wolcott
 * Dead Chest's Treasure
 * The Ghost Ship
 * Mad Doctor's Castle
 * Oak Island

Others

 * The Ruins at Cerros

Trivia

 * In the tomb hidden in the Santa Maria della Visitazione, if Ezio activated the lever and stood on the edge of the floor to stare into the water for a minute, he would see a large figure move through the water and stare at him with what appeared to be a yellow eye. After the cutscene, the lever would reset, allowing Ezio to activate it again. If he did so and returned to the same spot, a giant tentacle would shoot out of the water, though the Assassin would dodge it.
 * In Amunet's tomb at the Basilica di San Marco, the banners clearly showed the poison seal, despite her Assassin seal bearing the symbol of a snake.