In 1998, the KMT fielded Ma to challenge the then-incumbent Taipei mayor Chen Shui-bian of the opposition Democratic Progressive Party (DPP), who was seeking re-election. Despite Chen's public approval rating of over 80%, he was defeated. In the 2000 Presidential Election, Ma remained loyal to the KMT and supported its candidate, Lien Chan, over James Soong, who had bolted from the party and was running as an independent. The competition between Lien and Soong split the Pan-Blue vote and allowed his former rival Chen to win the presidential election with less than 50% of the popular vote. The election result, combined with other factors, incited a great deal of anger against Ma when he tried to dissuade discontented Lien and Soong supporters from protesting by appealing to them in his dual capacities as Taipei City mayor and a high-ranking KMT member.
Ma was able to repair the political damage and, in December 2002, became the leading figure in the KMT by easily winning reelection as mayor of Taipei with the support of 64% of Taipei voters while DPP challenger Lee Ying-yuan received 36%. His solid victory, especially in light of opposition from both President Chen and former President and KMT Chairman Lee Teng-hui, led many to speculate about his chances as the KMT candidate for the 2004 presidential elections, although nothing came of it.
Ma again dissuaded angry Pan-Blue supporters from protesting, following the very close re-election victory of President Chen in 2004 after the 3-19 shooting incident. Ma chose not to join in calls to challenge or contest the election. Ma also avoided associating himself with claims that the assassination was staged.
Ma suffered some political damage as a result of the SARS epidemic in early 2003 and was criticized for not mobilizing the Taipei city government quickly enough and for keeping Chiu Shu-ti, the public health director, who was previously criticized for her lack of concern for the outbreak. Flooding in metropolitan Taipei in 2004 also led to public questioning of his leadership and caused Ma's approval rating to slide.
During his time as Taipei's mayor, Ma had many conflicts with the central government over matters such as health insurance rates and control of the water supply during the drought. Ma also was implicated in a scandal of Taipei Bank stock releases in 2003. However, the case was dismissed after an investigation by the Taipei prosecutor. He was strongly criticized by the DPP for not allowing the ROC national flag to be flown along with a PRC flag during Asian Women's Football Championship held in Taipei. Ma responded that he was merely following Olympic protocol, which only officially recognizes the Chinese Taipei Olympic Flag and forbids ROC national flags from being shown in an Olympic Game Stadium.
His initiatives in administering the city of Taipei include changing the transliterations of street names and the line and stations of the Taipei Metro to Hanyu Pinyin, as opposed to Tongyong Pinyin. Ma has expressed mild support for Chinese reunification and opposition to Taiwan independence. He opposed the 2004 referendum, which had been widely criticized by the U.S. and PRC. Nevertheless, his opposition to the Anti-Secession Law of the People's Republic of China, while other leaders of his party remained silent on the issue, led to him being banned from visiting Hong Kong to make a public speaking tour in 2005. He also criticized the PRC for the Tian'anmen crackdown.
Ma's cross-political following has led some to note him as a rare example of relative civility in the notoriously rough and tumble world of Taiwanese politics. Ma has generally avoided being accused of using the vitriolic and sometimes offensive rhetoric common in Taiwanese political debate. His academic background and bearing have helped cultivate the image of Ma as an honest, dispassionate technocrat. Despite this reputation, and his wooden speaking style and shy demeanor, Ma is also considered a charismatic figure and is popular among women and youth. On the other hand, Ma's critics claim that Ma, overeager to appear unbiased and/or neutral, is overly indecisive and lacks bold vision. Ma is often accused of avoiding being out in front on some of the more vigorous or controversial criticisms of President Chen or opposing parties, or involving himself in intra-party disputes. Among these critics, Ma has been referred to as a "non-stick pan" or "Teflon-man." Recently, there has also been some criticism of his stumping for election candidates suspected of and later indicted for corruption charges. Many in the Pan-Green Coalition expressed opinions that Ma misled voters by lending his clean charismatic image to unscrupulous candidates in his own party.
In recent years, Ma has increasingly employed Taiwanese (Hoklo) in public speaking, perhaps to avoid backlash for his parents' mainland China origins, and he has called himself a "child of Bangka (Wanhua)", identifying himself with the historic district of Taipei where he grew up. Others claim that Ma's mainland Chinese ancestry will further alienate members of the KMT who are "light-blue" vs. the pro-unification "deep-blue."
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