from wikipedia:

There is speculation that Mombasa held some significance to the Forerunners which is why the Covenant attacked the city. The fact that the Prophet of Regret was able to jump straight to Delta Halo afterward indicates that something must have been found while in Mombasa (possibly the Ark?), because the location of the Halos were a mystery to the Covenant. It is believed that the Scarabs were designed to be digging machines, and that they were digging for something in New Mombasa. There are 3 Scarabs in Halo 2, one in the campaign level Metropolis, one in the campaign level The Great Journey, and the other on the multiplayer map Turf. Many Scarabs have fallen in the narrow streets of Old Mombasa.

What is very interesting is also the proximity of New Mombasa to the Great Rift Valley, the evolutionary "birthplace" of the Human race, from where the earliest Humans migrated out into the rest of Africa and eventually the world. If Humans can be seen as the descendants of, or in any way biologically related to the Forerunners, then it is a possibility that an extremely ancient Forerunner facility of some kind is nearby (again, the Ark?). The teaser trailer for Halo 3 and the associated FAQ only strengthened this theory.

PS>>>the second paragraph about the gread rift valley is something i hadnt even thought about, and bungie has confirmed that the ruins in the backround of the halo 3 trailer is the ruins of old/new mombasa