Summary
The Ark is a mysterious Forerunner device from which all the Halos can be activated. In the end of Halo 2, Delta Halo is armed and then unexpectedly shut down, causing it to send a superluminal signal to all other Halos in the galaxy, putting them on standby mode. 343 Guilty Spark informs Miranda Keyes and Sergeant Johnson that the Halos must now be activated from "The Ark". The location of the Ark is speculated as being on Earth, buried under the African soil near New Mombasa. It has been proposed that the effect of the ship commanded by the Prophet of Regret jumping into slipspace inside the Earth's atmosphere had a devasating effect on everything around it. This caused the destruction of New Mombasa, and aided in unearthing "The Ark". Whether this effect was intentional or coincidental is all specualtive at this point.
In the Halo Graphic Novel, Second Sunrise Over New Mombasa, a transmission is intercepted between the Covenant assualt forces stating that once the humans have been dealt with, they would start uncovering the Ark, offering further proof that the Ark is most likely on Earth and located under the New Mombasa area.
It is expected that Halo 3 will reveal more details about the Ark. The Halo 3 Announcement Trailer depicts the Ark firing a beam of white energy straight into the sky, through the center of swirling clouds. This structure can be confirmed to be the Ark from a concept sketch found in the DVD (seen right). The structure in the Halo 3 Announcement Trailer has not officially been announced as the Ark by Bungie however.
It is also believed, though this is purely speculative, that the Ark may have sheltered the Forerunners after Halo's first use, which then evolved into humanity. In the Bible, God floods the Earth to cleanse it of all life, which has grown evil and wicked. However, he saves a group of righteous humans and two of of all animals by telling them to build and seek refuge in a ship, called the Ark. Thus it is a possibility that in Halo, the Ark is a structure or device that shields those using it from the effects of the rings' activation and the Flood. The humans on Earth might have descended from those who were protected by the Ark during the first activation of the rings. This theory is purely speculative of course.
Another speculative opinions rests that the Ark is a forerunner ship which would jump into slipspace at the time of the activation of the seven Halo rings, thus removing the occupants from mass genocide that would purge the galaxy of all sentient life.
Trivia
The name of the Ark may refer to the biblical story of Noah's Ark (Genesis, chapter 7) that was built to save Noah's family and a number of animals from a massive flood, "the ark saves humanity from the flood." However, it's possible that it has a double meaning referencing to the Ark of the Covenant. In the old testament, the Ark of the Covenant, which contains the stone tablets of the ten commandments, is the holiest object of the Jewish faith and is a powerful weapon for the Jewish nation. This is supported by the location (east Africa), which is popularly believed to be the final resting place of the Ark.