Bloemfontein – Former National Prosecuting Authority head Mokotedi Mpshe's decision not to prosecute President Jacob Zuma for graft was rational, court papers argue.Zuma has filed his replying affidavit to the Supreme Court of Appeal in Bloemfontein, challenging a High Court ruling that he should face corruption charges.According to the affidavit, Mpshe had considered that the public interest, for declining to continue with the prosecution, outweighed the merits, and that "this was perfectly rational"."The DA seek to view the timing manipulation by [Leonard] McCarthy (in consultation with former NPA boss Bulelani Ngcuka) as a decontextualised insulated incident which was all Mr Mpshe was to consider," the affidavit reads.It argued that the party [DA, in its affidavit to the court] had postulated that Mpshe had to "close his eyes" to the role that then-Scorpions boss McCarthy and Ngcuka had played in the Zuma matter."It is incorrect that it will be unnecessary for this court to decide the question as to whether or not the NPA may as a matter of legal principle, discontinue the prosecution of the basis of allegations of abuse of process."Specific instructions from NgcukaIn regard to the DA's allegations relating to the timing of the prosecution, the affidavit said that the record and the transcripts demonstrated that, without Mpshe's knowledge, the two had decided to delay serving the indictment because they believed that Mbeki's chances of beating Zuma at the Polokwane conference would be strengthened.It was decided that the indictment would be served after the conference."After Mr Zuma was elected as ANC president, Mr McCarthy expedited the prosecution out of concern that Mr Mbeki would be recalled as President and the prosecution would be aborted."Mr McCarthy took specific instructions from Mr Ngcuka after Mr Mbeki was unsuccessful at Polokwane."Zuma argues further that the DA couldn't contest that the matter raised issues of public importance, and that leave to appeal was justified. In June, the High Court in Pretoria dismissed Zuma's leave to appeal its corruption decision.Prosecution would have been in bad faithThe NPA and Zuma's lawyers wanted leave to appeal the court's ruling on April 29 that the decision to discontinue the prosecution against Zuma on 783 corruption charges should be reviewed and set aside.Judge Aubrey Ledwaba said that Mpshe had acted irrationally after coming under pressure.Hilton Epstein, for the NPA, argued before the court earlier this month that Mpshe would have acted in bad faith if he had continued with the prosecution, knowing there had been an abuse of the prosecutorial process.On April 6, 2009, Mpshe said transcripts of telephone conversations between McCarthy and Ngcuka showed political interference in the decision to charge Zuma.The charges were withdrawn in the High Court in Durban on April 7, 2009.