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In a ruling delivered in open court on December 29, 2025, presiding judge Justice Emmanuel Baguma dismissed an application seeking a stay of proceedings in Criminal Session Case No. 335 of 2025, as well as a request for bail, directing that plea-taking should proceed immediately.

“It is therefore my view and opinion that for the interest of justice to both parties, the Applicants should proceed to take plea,” Justice Baguma ruled.

“If they so wish, they can apply for bail at any later stage if there is any delay in hearing of their case. I am aware and alive to the constitutional right of presumption of innocence of the Applicants until proven guilty.”

The judge faulted the defence for repeatedly filing interlocutory applications instead of responding to the substantive charges, noting that the case had stalled for months as a result.

“According to the court record, the Applicants were committed on 29th May 2025 and the matter was fixed for plea taking on 1st September 2025, but to date the Applicants have never taken plea,” he said.

“Instead, they resorted to filing applications after applications, making the process of plea taking difficult.”

Justice Baguma concluded that the application for stay of proceedings and bail lacked merit and dismissed it in its entirety.

“In the final result, and for the reasons stated above, this application for stay of proceedings in Criminal Session Case No. 335 of 2025 and releasing the Applicants on bail is dismissed,” he ruled.

The decision has sparked debate within legal circles, with some lawyers including Ferdinandius Loyola describing it as a new procedural precedent.

“Every day we get new precedents. Even though the Constitution and the Guidelines for Bail provide for applying for bail at any time after being charged, the new precedent is that: apply for bail after plea taking. The reason this is a new precedent is because the judge didn’t cite any single authority in support,” says lawyerLoyola

While Uganda’s Constitution and bail guidelines allow an accused person to apply for bail at any stage after being charged, the court effectively held that plea-taking must come first.

Despite the court’s directive, Dr. Besigye and Hajji Lutale declined to take plea, arguing that the indictment before court is fundamentally flawed and cannot form a lawful basis for trial.

Through their lawyers Erias Lukwago and Martha Karua, the accused challenged the validity of the indictment, stating that it was neither signed nor dated by the Registrar of the High Court as required by law.

The defence further pointed to alleged inaccuracies in the personal details and particulars of one of the co-accused, Capt. Dennis Ola, arguing that these defects rendered the charge sheet incurably defective.

Mr. Lukwago told court that proceeding with plea-taking on such an indictment would amount to a miscarriage of justice and urged the judge to halt the process until the defects were addressed.

However, the prosecution strongly opposed the objection.

Assistant Director of Public Prosecutions Thomas Jatiko, alongside Chief State Attorney Richard Birivumbuka, insisted that the accused must first enter plea, arguing that any errors on the indictment could be rectified through amendments during the trial.

After hearing both sides, Justice Baguma directed that the accused be returned to court the following day, when he is expected to rule specifically on whether the indictment is defective as alleged by the defence.

Dr. Besigye and Hajji Lutale are facing treason charges arising from what prosecutors describe as a coordinated plot to overthrow the government of Uganda between 2023 and 2025.

According to the indictment, the accused are alleged to have played central roles in organising meetings, mobilising financial resources and collecting intelligence in furtherance of the plot.

The prosecution claims that the alleged activities took place in multiple international locations, including Geneva (Switzerland), Athens (Greece), Nairobi (Kenya) and Kampala.

The two have been held on remand at Luzira Prison for over a year following their arrest in Nairobi in November last year, a detention that continues to draw scrutiny from human rights groups and opposition supporters.

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Delivering a detailed ruling on Friday, October 3, 2025, Justice Chacha Mwita dismissed a preliminary objection filed by Lagat and the National Police Service (NPS), ruling that the court indeed has jurisdiction to hear and determine the constitutional issues raised in the case.

Through lawyer Cecil Miller, Lagat had argued that the case was wrongly filed before the High Court and should have instead been lodged at the Employment and Labour Relations Court (ELRC), as it allegedly concerned internal administrative decisions within the police service.

Miller, representing Lagat and the NPS, submitted that the decision by the DIG to step aside for 18 days and appoint his Principal Assistant Patrick Tito to act in his position was an internal human resource matter — purely administrative in nature and not constitutional.

He maintained that under the National Police Service Act and Service Standing Orders, the DIG was within his mandate to temporarily step aside and assign duties to another officer to ensure continuity of command within the police structure.

“The petition raises issues that touch on the administration and internal management of the police service,” Miller argued. “It does not raise constitutional questions but concerns the respondent’s right to exercise discretion within the confines of his office.”

The Attorney General, appearing for the NPS and the Inspector General, supported Lagat’s position, insisting that the High Court lacked jurisdiction since no constitutional right had been violated.

The State Law Office maintained that the petition amounted to interference with the internal management of the National Police Service.

However, the petitioner, Eliud Matindi, a UK-based activist, opposed the objection, insisting that the petition raised serious constitutional questions on whether a Deputy Inspector General can legally step aside from a constitutional office and unilaterally appoint someone to act in his stead.

Matindi argued that Lagat’s decision to step aside and appoint Tito was unconstitutional since the power to appoint or designate an acting Deputy Inspector General is vested only in the President, upon the recommendation of the National Police Service Commission (NPSC),not in the hands of the office holder himself.

In his ruling, Justice Mwita sided with the petitioner, finding that the case raises substantive constitutional questions deserving full hearing.

“I am unable to agree with the respondent that this court has no jurisdiction. I affirm that this court has jurisdiction. The preliminary objection is overruled,” Justice Mwita declared.

He went on to explain that the core issues in the petition were not about employment disputes or workplace grievances but about the interpretation and application of the Constitution, particularly regarding the powers and limits of a constitutional office holder.

“The issues raised do not include determination of employer-employee relationship or related matters,” the judge said.

“Rather, the issues are purely on the interpretation of the Constitution and the law, namely whether the first interested party’s actions were constitutional and legal.”

Justice Mwita further emphasized that the position of Deputy Inspector General is established by the Constitution, not the Employment Act, and therefore carries constitutional, not contractual, responsibilities.

“The position of Deputy Inspector General and the manner of appointment having been created by the Constitution has a constitutional connotation,” he ruled.

“The holder of that office is not an employee in terms of the Employment Act to make this petition fall within the jurisdiction of the Labour Relations Court.”

Citing Article 165(3)(b) of the Constitution, the judge reiterated that the High Court has the express mandate to interpret the Constitution and determine whether any act or omission violates it.

“Under Article 165(3)(b) of the Constitution, this Court is expressly mandated to hear any question on the interpretation of the Constitution, including determining whether anything said or done under the authority of this Constitution or any law is inconsistent with or in contravention of the Constitution,” said Justice Mwita.

He explained that the questions raised — such as whether Lagat could legally step aside and appoint an acting deputy — fall strictly within the High Court’s jurisdiction.

“This Court will have to determine whether anything that was said or done by the first interested party under the authority of the Constitution or the law is inconsistent with or in contravention of the Constitution or the law,” he stated.

“In other words, the petition seeks this Court’s determination whether the first interested party’s actions were within the framework of the Constitution and the law.”

Justice Mwita also quoted Section 9 of the National Police Service Act, which provides that both Deputy Inspector Generals — in charge of the Kenya Police Service and the Administration Police Service — shall be appointed in accordance with the Constitution and upon recommendation by the NPSC.

“The position of Deputy Inspector General and the manner of appointment having been created by the Constitution and reinforced by statute, has a constitutional connotation, and therefore, the holder is not an employee under the Employment Act,” he emphasized.

In his concluding remarks, Justice Mwita dismissed the objection by Lagat and the NPS.

“In these circumstances, I am unable to agree with the Respondent and First Interested Party that this Court has no jurisdiction to hear this petition. Rather, I affirm that this Court has the jurisdiction to hear the petition. Consequently, on the conditions stated above, the preliminary objection is overruled and dismissed with no order as to costs.”

The court has now directed that the case proceeds to a full hearing where the substantive questions will be addressed,including whether the DIG’s step-aside was legally valid and whether his appointment of an acting deputy was within his constitutional powers.

The matter will come up for mention on November 17, 2025, for the parties to file and highlight their written submissions.

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In a replying affidavit filed at the Milimani High Court Constitutional and Human Rights Division, EACC’s Director of Legal Services and Asset Recovery, David Too, confirmed the agency’s support for the presidentially-established Multi-Agency Team on War Against Corruption (MAT-WAC), despite its leadership by the Executive Office of the President.

“The EACC is therefore, in principle, in favour of MAT-WAC framework so long as the independence of the Commission is safeguarded,” said Too in the affidavit.

This admission comes in response to a petition filed on August 20, 2025, challenging the legality and constitutionality of the new team, whose establishment was announced via a Presidential Proclamation on August 18, 2025.

The proclamation brought together 11 institutions, including the Directorate of Criminal Investigations (DCI), National Intelligence Service (NIS), Kenya Revenue Authority (KRA), Office of the Director of Public Prosecutions (ODPP), and the EACC itself.

The inclusion of the Executive Office of the President as Chair has drawn scrutiny, with petitioners arguing it threatens the autonomy of independent commissions.

But EACC downplayed those concerns, saying: “Independence does not mean acting in isolation from other state organs,” stated Too.

“The Commission is required to collaborate with other state agencies in the exercise of its mandate since the fight against corruption requires all hands on deck.”

Too further defended EACC’s participation in MAT-WAC by citing multiple legal and policy frameworks supporting inter-agency cooperation, including Section 11(3) of the EACC Act, Article 38 of the United Nations Convention Against Corruption, and Supreme Court precedents.

“Collaboration creates synergy while leveraging on the unique strengths of each entity,” he noted.

“This prevents inefficiencies, missed opportunities, and operational failures.”

Despite reaffirming EACC’s status as a constitutionally independent commission under Article 249(2) of the Constitution, the affidavit emphasized that “integration, linkages, partnerships, teamwork” are critical tools in a modern, whole-of-government anti-corruption strategy.

However, legal experts others argue the statement that EACC is “ready to work under” a team chaired by the President’s office could set a dangerous precedent.

“This is more than just collaboration. It borders on surrendering autonomy,” said a constitional lawyer  familiar with the case, who requested anonymity.

In his affidavit, Too emphasized that the anti-graft body’s involvement in MAT-WAC is not a constitutional compromise but a strategic necessity.

“The members of MAT-WAC are institutions with crucial information that could expedite investigation and prosecution of corruption offences and recovery of assets obtained from corrupt activities,” he said.

The petitioners, led by activist Dr. Magare Gikenyi, are seeking a declaration that the presidential proclamation violates the Constitution by compromising the independence of commissions like the EACC.

They claim that the president has ursuped the mandate of constitutional offices including EACC, ODPP and the graft Taskforce is therefore illegal, and unconstitutional.

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