The Ark is a vessel that the Survivors have been building to carry them out of the Void. Its exact location is unknown to the Watchers, and is a closely guarded secret among the Survivors. It was designed by Nikola Tesla.
The Ark is kept afloat by propulsion generators located on its sides (these generators apparently create some kind of electromagnetic field that allows The Ark to float), and it is outfitted with turrets and AA Guns all over its hull. This immense firepower, however, is counteracted by the fact that it moves incredibly slow (even with its very large engines that are located at its bottom).
After the prison break level, the Watchers finally find The Ark (after following the Survivors from the prison), and Will is forced to defend it using anything at his disposal, which include AA guns and Survivor Aircraft.
After a fire in the engines disables the propulsion generators and leaves The Ark grounded, Will must recharge them using the Hypercoil in order to allow The Ark to take off and escape from the Watchers.
The reason the engines caught on fire is because The Ark is a massive vessel made from salvaged technology, and much of this salvaged technology was very quickly and haphazardly put together due to the limited amount of time the Survivors had before the Watchers found The Ark's position and attempted to destroy it.
Will must then break The Ark's docking clamps using the guns on his rocket pack in order to FINALLY allow it to take off; he must then protect it from three Archons. This stage is made much harder by the fact that The Ark moves so slowly and therefore takes damage very quickly; the best advice for this stage is to quickly take out the three Archons by flying high above them, then dive-bombing them with the rocket pack's machine guns (or use magnetic rockets if you have purchased that upgrade).
After this battle, Will and The Ark finally escape from the Watchers. However, the Watchers catch up to The Ark near the Broken Land, and Will must defend it again, this time using Survivor Airplanes and/or his own jetpack to take out the Watcher Flying Discs and Watcher Transports surrounding The Ark. He must also make sure that he takes out several Watcher Stationary Turrets, Watcher Mines, and Archons that are located in the ravine that The Ark is passing through.
At the end of this escort mission, you are required to defend The Ark from a Watcher Battleship, which is a very formidable enemy outfitted with Watcher Mines, Watcher Stationary Turrets, and Watcher Flying Discs. To take this new enemy out, focus on the turrets covering its exterior first; also, take care of any Discs it may launch during this period of time. Make sure you also take care of the Watcher Mine Turrets embedded in the hull of the vessel, which not only fire shots at you, but can also be launched in your general direction as an actual mine, making them a very dangerous weapon if ignored.
After destroying all of these turret mines, you can finally exploit the Battleship's weak points at the ends of the craft (due to the fact that the shields surrounding them have lowered because of the destruction of the mines, which were apparently powering the shields). By rewiring two control panels at both ends of the vessel, you can cause the power cores to come out from the hull of the ship; shooting these power cores destroys the entire ship, and ends the mission.
At the beginning of the next level, Will and The Ark are trapped by a gigantic (even more massive than The Ark), non-sentient being known as The Collector, and all of the Survivors face digestion unless Will can find a way to destroy it.
In order to kill The Collector, Will must shoot the bubble-like masses at the center of the being, which opens it back up and allows The Ark to escape. Make sure you kill the shrimp-like organisms that The Collector spawns too, as they can "shoot" you and make you take large amounts of damage.
After escaping from The Collector, Ava and Will have a talk about where they are going (the Broken Land), how she believes that Nikola Tesla is The Key, and how he must hear the Imperator's message in order to save the human race from the grip of the Watchers. However, unbeknownst to both of them is the fact that "Tavi" (aka a Watcher imposter) has been listening in on this conversation. This imposter later decides to take the form of Nikola and, whilst the real Nikola's back is turned, stab and kill him with a knife.
After these events transpire, the imposters allows his fellow Watchers to infiltrate the ship; one of these infiltrators knock out Will, and it seems as if the entire Ark is taken prisoner.
Now a prisoner in the Watcher Base, Will is eventually rescued by Atem, who says that the Survivors had contingency plans if The Ark was ever infiltrated. After escaping from the base, it is shown that the Survivors recovered The Ark (with the Imperator now aboard), and that the revolt in the Broken Land has begun. The Ark will be helping out the revolters, whilst Ava, Will, and a couple of other Survivors go to try and close the Tower of Return's Gateway to Earth.