Russian President, Vladimir Putin, immediately cancelled his Siberian vacation upon hearing news of the hijack, and set to deal with the incident. It was reported that the Federal Security Service, the FSB, immediately started putting together a team to take down the airplane if the opportunity arose. The force was "two planeloads" strong, according to a CNN report, and was ready to depart at a moment's notice. By this time, the hijackers had diverted the airplane to Saudi Arabia, and forced it to land at the airport in Medina, one of Arabia's holiest cities. The airplane was isolated from the rest of the airport, sitting by itself away from the main airport area. Meanwhile, FSB negotiators attempted to establish a dialogue with the terrorists, suspected to be Chechen separatists. In conflicting reports, the Russians reported that they were in direct contact with the pilots, who had managed to barricade themselves in the cockpit. At this time, Saudi officials, also negotiating with the hijackers, revealed that the total number of hijackers was four, rather than the original two. Furthermore, the hijackers issued their demands, an end to the Russian counter-terrorist campaign in Chechnya. Initially, a Chechen rebel spokesman denied involvement in the incident, but the rebels identified the hijackers as former Chechen Interior Minister, Aslambek Arsayev, and his brother, at a later time.

On March 16, negotiators succeeded in securing the release of 47 hostages, mainly women and children, and the steward who was stabbed during the initial minutes of the hijack. Negotiations resumed to gain the release of the 100 plus hostages still on board of the Tu-154. In a turn of events that same day, negotiations broke down, and Saudi officials, along with approval of the Russians decided to storm the airplane, after the hijackers threatened to blow up the airplane, and demanded it be refuelled for a suspected flight to Afghanistan.

Broadcast on Saudi television, commandos dressed in camouflage fatigues and tactical vests and helmets, stormed the airplane, and secured the airplane and the hostages, but at the cost of the deaths of two hostages and a hijacker. A female flight attendant, and a Turkish passenger were killed during the rescue. After the airplane was secure, television showed two men being handcuffed on the tarmac, establishing the number of hijackers at three. The ordeal was over.

Russia is presently seeking the extradition of the two hijackers, and are awaiting the return of the airplane to Russia. The Russian government has accused both Turkey and Saudi Arabia of co-operating and supplying the Chechen rebels seeking independence from Russia.