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1985–2012: Fall of the original Cosmos and revival

The original New York Cosmos club began play in 1971 in the original North American Soccer League. The league ceased operations after the 1984 season, and the Cosmos were dissolved in 1985 after playing a season in the Major Indoor Soccer League. Peppe Pinton, managing director for the Cosmos at the time, continued to run and operate youth camps started in 1977 and named after the club's stars.

With the rise of Major League Soccer (MLS) during the late 1990s and 2000s, MLS had an interest in placing a second club in the New York market. In 2007, a supporters group named the "Borough Boys" was formed to push for a team in New York City itself, and in his 2010 "State of the League" address, Commissioner Don Garber confirmed that was indeed the goal. In the meantime, the original Cosmos were the subject of an ESPN documentary, Once in a Lifetime: The Extraordinary Story of the New York Cosmos, introducing the name to a new generation of fans. Garber also stated at one point that if MLS was to have a second New York club, it would be the Cosmos, and various New York City area entities approached Pinton about using the name. Even the existing MLS club in New York, the MetroStars, made relevant inquiries both before and after becoming the New York Red Bulls in 2006.

Pinton was initially reluctant to let the name be used by an MLS team, believing that the league was unwilling to respect the Cosmos' heritage; however, after seeing MLS reintroduce historical NASL names such as Seattle Sounders FC, Vancouver Whitecaps FC, and Portland Timbers, he changed his mind. In late August 2009, Pinton sold the name and image rights for $2 million to Paul Kemsley, the former vice-chairman of English Premier League club Tottenham Hotspur, who headed a group intent on establishing a new Cosmos team in MLS. At the time, Kemsley was best known as a failed property magnate and an assistant to Alan Sugar on the British version of . The ownership group announced the club's return on August 1, 2010.

Kemsley's group included English soccer businessman Terry Byrne as vice-chairman, as well as former Liverpool CEO Rick Parry. The investors funding the venture were rumored to be Saudi Arabian, although the full ownership group was not publicly announced at the time.

One person familiar with Kemsley's plans for the Cosmos said his intention was "to build the brand and then build the team around that. It will not be cheap, it may not work, but it will be interesting."

To that end, Kemsley signed a deal with Umbro to produce a line of merchandise, including tshirts, jackets, and a "home jersey". Umbro followed this collection with a second "Blackout" line of Cosmos clothing in all-black with monochromatic black logos, supposedly inspired by the New York City blackout of 1977. The Blackout collection was unveiled at a pop-up shop on the Lower East Side, featuring a DJ playing period songs from 1977. With two full fashion lines before the club had joined a league or signed a single player, some journalists viewed this new Cosmos as a "money-grab" more interested in "selling shirts" than actually playing soccer.

The group's first high-profile hiring was former United States player Cobi Jones as associate director of soccer, followed by Eric Cantona, who was hired as director of soccer in mid-January 2011. Cantona claimed "big plans" to build the club around homegrown talent, although the club would later claim in court that Cantona had never been given any actual responsibilities with the club, that he had only been a promotional figurehead. Jones left the club in 2012, and Cantona was fired from his role shortly thereafter. Neither departure was officially announced by the Cosmos.

The new team sought connections with stars from the original Cosmos team. One of their first acts was to sign Pelé to a five-year, five million dollar promotional contract as the team's "honorary president", and original Cosmos players Shep Messing, Carlos Alberto, and Giorgio Chinaglia were named "international ambassadors" for the club.

The new Cosmos' first match was on August 5, 2011, when they played in Paul Scholes's testimonial match against Cantona's former club Manchester United at Old Trafford. Cantona managed the Cosmos, with a roster consisting of a team of guest players from around the world.

On October 26, 2011, Kemsley sold his shares to the co-owners, revealed to be Sela Sport, a Saudi Arabian sports marketing company. The departure of Kemsley was announced by the Cosmos with an official club statement saying that he wished "to pursue other interests and commitments", while the New York Post reported that he had been ousted by his partners, with Sela "apparently tired of the flamboyant Brit, who was long on flash but has to this point been short of substance". His replacement was not immediately announced. A further press release on November 2 gave news of the company buyout, restructuring and various unspecified management changes within the organization. The statement also said that the goal of the club remained the same under its new structure – "unequivocally" to become an MLS team. Around the same time, the entire unsold stock of Umbro merchandise was sold to a discount retailer "for pennies on the dollar".

Within weeks of his appointment, new chairman and CEO Seamus O'Brien had a series of meetings with MLS commissioner Don Garber about joining Major League Soccer. Garber was still eager to add the Cosmos to MLS, and offered O'Brien a spot in the league, but O'Brien balked at the $100M expansion fee, single-entity structure, and requirement that the league control the brand. O'Brien decided not to apply for MLS entry after all.

2013–2015: Return to competitive league play

The Cosmos announced on July 12, 2012, that they would start competitive play in the second-tier North American Soccer League in 2013, but insisted in the same press release that the club was still bent on ultimately joining MLS. In November, Erik Stover was hired as the club's Chief Operating Officer. Stover had previously been managing director of the New York Red Bulls, during which time he had been named MLS Executive of the Year, and was seen as instrumental in getting their stadium built. The following week, Giovanni Savarese was confirmed as the team's first head coach. On December 11, former Red Bulls defender Carlos Mendes, a native of Long Island, became the new Cosmos' first senior player.

The Cosmos found immediate success in the NASL, winning the Fall Season Championship with a 9–4–1 (Win-Draw-Loss) record. On November 9, 2013, the team emerged as the winner of Soccer Bowl 2013, winning 1–0 against the spring season champions, the Atlanta Silverbacks. In June 2015 the New York Cosmos played a friendly against the Cuba national team, the first U.S. professional club to play in Cuba after the United States began normalizing relations with the island nation.

Despite that on-field success, the Cosmos struggled to draw fans at Hofstra.

In 2015, Cantona sued the club, claiming that they had failed to pay him almost one million dollars in salary and a four percent equity interest he had been promised. The parties settled in March 2017. Details of a potential settlement were not initially disclosed, although it later reported that Cantona received £780,000 from the Cosmos.

After the Cosmos won the 2016 NASL Championship Final, supporters publicly called for a meeting with the club's owners, citing a lack of transparency from management and concerns over the club's future.

2016–present: Financial struggles and sale

In November 2016, there were reports the team was in dire financial condition, including furloughs for 60–80% of the staff and an inability to make payroll. Later reports indicated that the Cosmos had lost over thirty million dollars since beginning play in 2013, including as much as $10 million in 2016. The Guardian pointed out that "(d)espite the team’s on-field achievements, the Cosmos have been plagued by mismanagement, dwindling attendance and practical irrelevance in the New York market."

On December 6, 2016, various media outlets began reporting that the Cosmos had released all players and coaching staff from their contracts, and that office staff had not been paid in up to six weeks. Cosmos supporters launched an online campaign to raise funds for affected employees. On December 9, most of the club's employees were officially laid off.

In an interview with the Guardian, O'Brien admitted the financial losses but denied that the club was in danger of going out of business, insisting that they had "zero debt". Empire of Soccer pointed out that while O'Brien was saying that, the Cosmos were being sued for over $50,000 in unpaid rent on their Garden City, Long Island offices. Despite O'Brien's public statements, the team came within a few hours of going out of business altogether, as he came to an agreement to sell the Cosmos brand to a private equity firm. On December 15, 2016, the day O'Brien was to finalize that deal, he began negotiations with Rocco B. Commisso, a cable television executive with a lifelong interest in soccer. On January 10, 2017, it was announced that Commisso purchased the majority interest in the Cosmos. His investment kept the club and league from folding and allowed both to return for the 2017 NASL Season. ESPN reported that O'Brien and Sela Sport retained a minority stake in the club, although supporters claimed that Commisso assured them that Sela Sport was no longer part of the ownership.

On December 13, 2017, the Cosmos announced that Savarese had left the club "to pursue other coaching opportunities".

Following the cancellation of the NASL's 2018 season, the league announced that the Cosmos would take a hiatus while exploring options to return to the field in 2019. In September 2018, Chief Operating Officer Erik Stover stepped down to become the CEO of a local soccer academy. For the 2018 season, some of the Cosmos players joined the organizations second team, New York Cosmos B, in the National Premier Soccer League (NPSL) and did so again for 2019.

On November 15, 2018, the NPSL announced that the Cosmos would be a founding member in a new professional league, commencing with the NPSL Founders Cup tournament from August to November 2019, followed by a full league schedule in 2020 at either division 2 or 3 level. This however, never came to be and the Founders Cup was later renamed to the Members Cup which Cosmos B took part in.

On May 23, 2019, the team played its first game since 2017 against 2. Bundesliga side FC St. Pauli at Rocco B. Commisso Soccer Stadium, which New York won 2–1. On November 20, 2019, the club announced their intention of joining the National Independent Soccer Association for their Fall 2020 season.