Operation Noah's Ark was an Independent State Allied Forces operation to protect two Air Ixiom airliners, which were under fire from Erusean fighters. Aboard the airliners were the engineers responsible for Stonehenge's development. The scientists were attempting to defect to ISAF in exchange for crucial information that would assist the Allies in destroying the railgun network.
Sometime after the retaking of Istas Fortress, the ISAF was contacted by several of the engineers who were responsible for Stonehenge's development. The scientists and their families, who had been held under Erusean custody since the beginning of the war, decided to defect to ISAF and provide the Allies with information on Stonehenge's defensive capabilities. The engineers and their families boarded two civilian airliners—Air Ixiom Flights 701 and 702—that were en route to Los Canas, which was now under ISAF control following Operation Woodpecker. Erusea became aware of the engineers' plans and launched interceptors to covertly shoot down the civilian aircraft.
Flight 701 was hit by enemy fire during takeoff, injuring the captain and destabilizing the airliner's cabin pressure. First Officer Nagase took command of the aircraft and assumed an altitude of 6,000 feet to maintain pressure. Flight 702 took off without incident and reached a standard cruising altitude of 23,000 feet. When the airliners detected incoming Erusean aircraft on radar, ISAF immediately launched Mobius 1 on a solo escort mission to defend the aircraft and ensure the scientists' safe defection.
By the time Mobius 1 arrived at the location of the airliners, Flight 702 (flying at 23,000 feet) was being pursued by an Erusean F/A-18C Hornet. After shooting down the Hornet, Mobius 1 descended to 6,000 feet where two MiG-29A Fulcrums were firing upon Flight 701. Following their destruction, Mobius 1 climbed back to 23,000 feet where a squadron of three F-14A Tomcats were chasing Flight 702. The Erusean fighters broke off their pursuit, and after a short dogfight, Mobius 1 downed the attacking aircraft. As Flights 701 and 702 prepared to exit the hostile airspace, a final squadron comprised of two Su-35 Flanker-Es and two more MiG-29As appeared at 6,000 feet and engaged Flight 701. After Mobius 1 shot them down, AWACS SkyEye scanned the area and determined that the airspace had been cleared of hostile Erusean fighters.
Flights 701 and 702 successfully landed at an ISAF air base, where ambulances and fire engines were standing by. The passengers and crew were examined by an ISAF medical officer, who determined all were in good health. Several ISAF-member states presented offers of amnesty to the defectors, who, in return, provided information that would prove helpful in formulating a second ISAF air strike on Stonehenge.
- Due to Flights 701 and 702 flying above 2,000 feet, Stonehenge itself could have been used to shoot down the airliners. It has not been explained why Erusea engaged the airliners with fighters instead. One theory is that using Stonehenge's rounds could have placed other civilian airliners in danger of being shot down.
- The operation's name references the religious real-life story of Noah's Ark.