Panathinaikos downfall continued as a result of the serious riots in the Panathinaikos–Olympiacos derby of 18 March 2012. The entire board quit and Panathinaikos remained headless for about two months. However, the owner of Skai TV, Giannis Alafouzos, devised a plan to take Vardinogiannis shares (54.7%) and make them available to fans around Greece so that everyone could contribute a desired amount

On 2 July 2012, the PAO Alliance 2012  finally opened to the public so that everyone could be a member and contribute a desired amount in return for privileges. After a few weeks of operation, 8,606 members had signed up, some of which were current or former Panathinaikos players, including Jean-Alain Boumsong, Sotiris Ninis, Gilberto Silva and Djibril Cissé, among others.
n 18 July 2012, marked a historical day in Panathinaikos history, as Giannis Vardinogiannis gave his shares—54.7% of Panathinaikos—to the Panathinaikos Alliance, thereby allowing Panathinaikos to have a fresh start with their own fans at the steering wheel, who through elections (amongst the members of the Alliance) they compose the Board of Directors and elect the clubs president. The first president elected was Giannis Alafouzos.

The first season with the Panathinaikos Alliance at the helm was nothing short of abysmal for the club. While still enduring financial troubles, Panathinaikos finished sixth in the championship and failed to qualify for the European competition for the first time in 16 years. For the 2013–14 season, the membership had risen up to 9,305 members. Starting the football year, both fans and journalists were very skeptical of Panathinaikos chances of a successful season, and many people expected the team to suffer relegation from the Superleague Greece.  In May 2013, Yannis Anastasiou was appointed manager, and he planned a team based on players from the Panathinaikos Youth Academies joined by experienced foreign players looking to revive their careers. Despite the early skepticism, Panathinaikos fans supported the team through the rough start, and the season turned out to be a massive success in light of the dire financial situation of the club and the young and inexperienced squad. The club finished fourth in the regular season and second after the playoffs (meaning they qualified for the 2014–15 Champions League), with Marcus Berg the top scorer of the team. Panathinaikos also won the 2013–14 Greek Football Cup after a 4–1 win over PAOK.

On 2 November 2015, after bad performances and a home draw with AEK Athens, manager Yannis Anastasiou was sacked and replaced by Andrea Stramaccioni. Further successive poor results under the latters reign, combined with loss of dressing room control, led to the dismissal of Stramaccioni on 1 December 2016, with former Panathinaikos player and Greece international Marinos Ouzounidis taking over the management at the club.On 24 April 2018 UEFA decided to exclude Panathinaikos FC from participating in the next UEFA club competition for which it would otherwise qualify in the next three seasons as a result of Financial Fair Play breaches

Giorgos Donis was announced as the new coach on 3 July 2018 and is responsible for the rebirth of the club to this day.

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