Internet entrepreneur Shinichi Nishikubo controlled the company from 2003 to 2015, when the carrier filed for bankruptcy protection after attempting a fleet and service expansion.

In 2003, with a fourth 767 dry-leased (leased without any crew members) from All Nippon Airways, it began service to Aomori and Tokushima.

It briefly considered a recapitalization led by Commerzbank but decided not to accept such an investment due to Air Do's issues with banks interfering in management.

[11] By using more efficient aircraft and systems developed in-house, Skymark attempted to undercut JAL and ANA on costs in order to offer lower fares.

[12] Skymark had a code sharing partnership with Japan Airlines starting with a Haneda-Osaka Kansai service in 2005–06,[10] and later on the Tokyo Haneda-Kobe route from Kobe Airport's opening in 2006.

[19] Nishikubo envisioned an unheard-of fully-flat product in economy class, which the Skymark team calculated would break even at a one-way fare of 100,000 yen.

[26] The Japan Federation of Cabin Attendants publicly complained about the idea, claiming that the uniforms were unsafe to the women wearing them and would lead to harassment and objectification.

Many of Skymark's major investments and expenses were denominated in dollars—including the A380 orders, the A330 leases and its fuel costs—while its domestic ticket revenue was in yen, and the airline did not engage in exchange rate hedging.

[12] In early February 2014, Skymark announced that it would downsize the Narita operation to only three destinations (Sapporo, Yonago and Okinawa).

He also expressed some reservations about the A330 fleet plan, stating that while the airline had funding in place for the first two aircraft, the third and subsequent deliveries could be impacted by the performance of Skymark's domestic operation as well as the success of its initial international service.

Nishikubo rejected this proposal in early July, believing there was a significant chance that Skymark would miss the target.

Nishikubo complained the airline was not given the opportunity to revise the contract, but simply received a fax notifying it of the termination.

It announced in November 2014 that it was exploring a cooperative relationship with Japan Airlines under which Skymark's 36 daily round trips to and from Haneda Airport would be code shared with JAL, subject to approval by the Ministry of Land, Infrastructure and Transport.

In January 2015, ANA refused to provide financial support to Skymark, and several investment funds also balked at the prospect of injecting cash into the company.

In an attempt to regain price competitiveness, Skymark introduced a fare of ¥8,000 on the Haneda-Fukuoka route, 1,800 cheaper than the next cheapest competitor, StarFlyer.

[35] Skymark was approached by several potential sponsors early in its bankruptcy proceedings, including ANA, AirAsia, Delta Air Lines and American Airlines.

[38] Skymark's restructuring plan, submitted to the court in May, called for turnaround sponsor Japanese private equity fund Integral to own 50.1% of the recapitalized company, ANA to own 16.5%, and the remainder 33.4% to be owned by an investment fund controlled by government-affiliated Development Bank of Japan and Sumitomo Mitsui Banking Corporation, with Integral providing the new chairman, DBJ providing the new CEO, and code sharing between Skymark and ANA.

[44] After exiting bankruptcy in 2016, Skymark's finances improved more quickly than expected; the company recorded 6.7 billion yen in operating profit in the March 2016 – 2017 fiscal year.

[46][47] Since 2020, due to the COVID-19 pandemic, the Saipan route was cancelled and was never restored; in late 2022, the CEO of Skymark publicly stated that the airline has no plans to resume scheduled international service before 2026.