[2] Megumi Yokota was abducted on 15 November 1977 at the age of thirteen while walking home from school in her seaside village in Niigata Prefecture.

[3] After many years of speculation and no new leads, in January 1997, information about Megumi's abduction was disclosed to Yokota's parents by Tatsukichi Hyomoto, a secretary to Diet member Atsushi Hashimoto,[4] by a phone call.

In November 2011 a South Korean magazine, Weekly Chosun, stated that a 2005 directory of Pyongyang residents listed a woman, named Kim Eun-gong, with the same birth date as Yokota.

[12] Japanese government sources verified on 18 November 2011 that they had reviewed the directory but had yet to draw a conclusion on the identity of the woman listed.

[16] In March 2014, the parents of Megumi Yokota met their granddaughter Kim Eun-gyong for the first time in Mongolia, along with her own baby daughter, whose father was not identified.

[17] Thae Yong-ho, North Korea's former Deputy Ambassador to the United Kingdom who defected to the South, claimed in his book Passcode to the Third Floor Secretariat that the controversy regarding the return of Yokota's remains was unexpected by Kim Jong-il and caused significant infighting between the ministry and Kim Jong-Il's staff, leading Vice-Minister for Foreign Affairs Kang Sok-ju to demand an explanation.

The Japanese Affairs Department of the Foreign Ministry internally published a report: Yokota Megumi died of a mental illness at the No.

[18]Thae believed that Kim Jong-Il, desperately wanting normalization of relations and economic aid, had not deliberately sent fake remains and was genuinely surprised by the resultant outrage from the Japanese press and the Koizumi government.

When the Japanese offer of normalization was rescinded, contingent on further progress over the abductions issue, Kim allegedly told Kang, "As expected, the Japs can't be trusted.

However, the death certificate provided in support of this assertion appears to have been falsified, and DNA tests on the remains said to be hers were not a positive match.

[2] An interview in the 3 February 2005 issue of Nature revealed that the DNA analysis on Megumi's remains had been performed by a member of the medical department of Teikyo University, Yoshii Tomio.

He said that he had no previous experience in the analysis of cremated specimens, described his tests as inconclusive, and remarked that such samples were very easily contaminated by anyone coming in contact with them, like "stiff sponges that can absorb anything".

When the Japanese government's Chief Cabinet Secretary, Hiroyuki Hosoda, referred to this article as inadequate and a misrepresentation of the government-commissioned analysis, Nature responded in an editorial (17 March), saying that:[19] Japan is right to doubt North Korea's every statement.

On 10 October 2011, Japan Today reported a defector had asserted that Yokota was still alive, but that she was not allowed to leave North Korea because she was in possession of sensitive information.

[23] On 19 September 2017, U.S. President Donald Trump, in a speech to the United Nations General Assembly, included Yokota in a series of accusations against the North Korean government, saying, "We know it kidnapped a sweet 13-year-old Japanese girl from a beach in her own country to enslave her as a language tutor for North Korea's spies."

Yokota's mother Sakie said, "I was really surprised, but it was great, and I'm thankful to (Trump) for bringing up the issue and putting it into words in front of those representatives from around the world.

"[24] It was reported that Trump sent a letter expressing his condolences to Sakie over the death of her husband Shigeru Yokota, who died on 5 June 2020, at the age of 87.