The Great Ark is a massive ship designed to house all remaining life on Earth. It is commanded by the Silver Surfer. It's mission is much like that of Noah's Ark, save all life on the planet so that it can start anew. It was made when Marduk was to once again wipe out the human race.
The Great Ark is incredible large. On board it has it's own zoo and ocean to contain the animals of Earth. It is also designed to make the children selected by the Silver Surfer content with their new lives and to forget their lives on Earth.
The Great Ark is controlled by a form of artificial intelligence and navigated by the Silver Surfer.
When Gabe Acheron took control of the ship, it crash landed in the Pacific Ocean. Everyone on board was killed, but this reality was erased by Ellie Waters. Essentially, it was made that Marduk never came so the Great Ark never needed to exist.