No case better illustrates the stakes in Uganda’s constitution and rule of law than that of Dr Kizza Besigye, the veteran opposition leader.

In November 2024, Besigye was picked up in neighbouring Kenya, taken across the border and charged before a military court with possession of pistols and attempting to purchase weapons abroad – charges he denied.

His appearance before the General Court Martial exemplified everything critics had long argued about military justice. The tribunal was composed of military officers, not independent judges. Its procedures were opaque. Its connection to the military chain of command raised inevitable questions about its impartiality.

Following the Supreme Court’s January 2025 ruling, Besigye’s case was transferred to a civilian court. The military charges were dropped and replaced with treason charges in the civilian system. Yet by the end of 2025, Besigye had been denied bail four times and had spent over a year on remand. The shift from military to civilian jurisdiction had changed the forum but not the fundamental dynamic: a prominent opposition figure facing serious charges in a highly politicised environment.

For human rights lawyer Gawaya Tegulle, the Besigye case illustrated precisely what was wrong with military courts:

“If you are a political opponent then they will find a way of getting you under the military court and then you know your fate is sealed… once there, justice will never visit your door.”

He added that people can spend years in detention on remand as military courts await decisions from senior figures – decisions that may never come. Those who are tried and found guilty face harsher penalties than in civilian courts.

Abductions, disappearances and torture

Besigye case is not isolated. It forms part of a broader pattern of repression that has intensified as elections approach. The UN has documented a troubling rise in arrests and abductions, harassment and intimidation, torture and other ill-treatment of political opposition members.

Civilians continue to be detained in military barracks for years, often without trial – a practice the law explicitly prohibits but the state continues to tolerate. Prison conditions remain harsh, with high mortality rates from overcrowding, unsanitary conditions, malnutrition and disease. Local prisons, which receive no central government funding, are particularly dire.

Uganda Human Rights Commission’s 1997 findings on torture and illegal detention – documented decades ago – read like today’s headlines. The same regime that once investigated the crimes of Amin and Obote now replicates their methods.

Implications and meanings

For the Justice industry and its development

The military trials controversy has profound implications for Uganda’s justice sector. When Parliament overrides a Supreme Court ruling, it undermines the very concept of judicial finality. When military courts try civilians, it creates parallel justice systems with different procedures, different standards, and different outcomes.

The development of a coherent, professional judiciary requires predictability and respect for hierarchical authority. The Supreme Court is meant to be the final arbiter of constitutional questions. When its rulings can be effectively nullified by legislation, the entire system loses coherence. Lawyers cannot advise clients with confidence. Citizens cannot know their rights. Investors cannot assess legal risks.

Moreover, the military courts themselves lack the professional infrastructure of the civilian judiciary. They are not integrated into the structure of judicial education, professional development and peer review that sustains civilian courts. Their personnel rotate in and out of judicial functions, never developing the specialised expertise that adjudication requires. The result is a system that produces rougher justice – faster, perhaps, but also shallower and less reliable.

For good governance

Good governance requires clear lines of accountability and the subordination of all state institutions to constitutional order. The military trials controversy reveals a breakdown in both.

When the army assumes judicial functions over civilians, it blurs the line between military and civilian spheres. Soldiers who are trained to follow orders, to prioritise hierarchy and obedience, are asked to perform functions that require independence, impartiality, and critical judgment. The results are predictable: military courts become instruments of command, not forums for justice.

The controversy also reveals the weakness of Parliament as a check on executive power. The NRM’s dominance of the legislature means that presidential preferences reliably become legislative outputs. The UPDF (Amendment) Act was passed despite opposition protests, despite constitutional concerns, despite international condemnation. Parliament functioned not as a deliberative body but as a transmission belt for executive will.

Civil-military relations

A democratic society requires clear boundaries between civilian and military spheres. The military exists to defend the nation from external threats, not to police civilian populations or adjudicate civilian disputes. When soldiers try civilians, those boundaries dissolve.

The implications extend beyond individual cases. When civilians see soldiers as judges, when they experience the military as an institution of everyday governance, they internalise a particular relationship between citizen and state – one in which rights depend on the goodwill of armed men rather than the protections of law.

The military itself is transformed by this role expansion. Soldiers who sit in judgment of civilians come to see themselves as arbiters of civilian conduct, as guardians of public order, as superior to the messy compromises of civilian justice. This mind-set – the belief that military efficiency should override civilian procedures – erodes the professional military ethos and replaces it with something more political, more dangerous.

Constitutionality and the separation of powers

The military trials controversy is, at its core, a crisis of constitutionalism. The Constitution establishes three branches of government with distinct functions. The judiciary interprets the law. The legislature makes the law. The executive enforces the law. When the legislature passes a law specifically designed to override a judicial interpretation of the Constitution, it violates this separation.

Article 92 of the Constitution prohibits parliament from enacting legislation “to alter the decision or judgment of a court of law in a particular case.” UPDF (Amendment) Act was precisely such legislation: a legislative override of the Supreme Court’s decision in the Kabaziguruka case. Yet Parliament passed it, and the President signed it, and the constitutional prohibition became a dead letter.

The deeper question is what remains of constitutional government when its most fundamental rules can be so easily evaded. If Parliament can override judicial decisions by legislation, if the President can ignore constitutional limitations by invoking security, if the military can exercise judicial power without constitutional authorisation – then the Constitution becomes what the regime makes of it, not what the people enacted.

Mafia and the deep state

The concept of the “deep state” refers to permanent structures of power that operate beneath and beyond democratic control – security services, military establishments, intelligence agencies that pursue their own agendas regardless of elected officials. In Uganda, the military trials controversy illuminates the relationship between elected officials and this deeper structure.

On the surface, the UPDF (Amendment) Act was passed by an elected Parliament and signed by an elected president. This was democratic decision-making, formally speaking. But the substance of the decision – to expand military jurisdiction over civilians – serves the institutional interests of the military, not any discernible public purpose. It empowers military prosecutors, military judges and military commanders at the expense of civilian institutions.

This is how the deep state operates: not through coups and overt seizures of power but through the gradual accretion of authority, the normalisation of military functions in civilian spheres, the creation of parallel structures that answer to command rather than law. The military courts are such a parallel structure. They exist alongside the civilian judiciary, applying different rules, reaching different outcomes, answerable to different masters.

People of Uganda

The ultimate victims of this constitutional decay are the people of Uganda – not only those directly prosecuted before military courts, but all Ugandans whose rights depend on the integrity of constitutional order.

When the Constitution fails to constrain power, when judicial decisions can be overridden by legislation, when military courts try civilians without independent judges or fair procedures – then citizenship itself is devalued. To be a citizen is to possess rights that the state must respect. When the state can ignore those rights at will, citizens become subjects.

This is what we see unfolding in Uganda today: a process of de-citizenisation, in which the rights and protections of constitutional membership are gradually withdrawn. Freedom of assembly is restricted. Freedom of expression is suppressed. Political opponents are kidnapped and disappeared. The press is intimidated. The Internet is monitored and controlled. And through it all runs the thread of military justice – the ultimate symbol of civilian subordination to armed power.

Resistance and the future

Legal challenge continues

Uganda Law Society has pledged to challenge the constitutionality of the UPDF (Amendment) Act. National Unity Platform has already petitioned the Constitutional Court. The battle that seemed settled by the Supreme Court’s January ruling will continue.

The legal arguments are strong. Article 92 of the Constitution prohibits legislation that alters court decisions in particular cases. UPDF (Amendment) Act does exactly that: it reinstates a jurisdiction the Supreme Court ruled unconstitutional. The Act may also violate the right to a fair hearing guaranteed by Article 28, and the structural separation of powers embedded in the Constitution’s design.

But legal arguments, however strong, must ultimately be heard by courts – and courts are themselves vulnerable to pressure. Chief Justice may insist that he needs no courage to interpret the Constitution, but judges are human beings who read newspapers, who hear the speeches of presidents, who understand the consequences of defying power.

International dimension

Uganda depends on foreign assistance for approximately 51 per cent of government spending. This dependency creates leverage – leverage that the international community has been reluctant to use. Donor countries have expressed concern about the military trials legislation, but concern has not translated into consequences.

The UN has urged compliance with the Supreme Court’s decision. Human rights organisations have documented abuses. But without sustained pressure, without meaningful consequences for non-compliance, international appeals become background noise – noticed but not heeded.

Question of transition

Behind the immediate controversy over military trials lies a deeper question: what happens after Museveni? The personalist NRM that has governed Uganda since 1986 is built around a single individual. Its institutions, its procedures, its habits of mind are all shaped by the man who has led it for four decades.

The military courts controversy reveals how deeply this personalism has penetrated the state. The army’s power is the president’s power. Military jurisdiction expands when the president wants it to expand. Judicial independence exists to the extent the president tolerates it. Parliament legislates what the President desires.

This is not sustainable. No institution built around a single individual survives that individual’s departure. The question is what comes next: a genuine transition to democratic constitutionalism, or a continuation of the same system with a different face?

The answer depends, in part, on struggles like the one over military courts. Every successful defence of constitutional principle creates a precedent, a resource, a foundation for future resistance. Every defeat – every legislative override, every kidnapped activist, every civilian tried by soldiers – teaches lessons about power and its limits.

Beyond military trials – the wider erosion

The military trials controversy is one violation among many. To understand its full significance, we must see it in context – as part of a broader pattern of constitutional erosion that includes:

Restrictions on freedom of assembly, association, and expression. Students, academics, intellectuals, and politicians in alternative political parties all face constraints on their fundamental rights. The space for public discourse shrinks year by year.

Electoral irregularities and suppression of opposition. Elections are conducted under conditions that favour the incumbent. The army explicitly or implicitly sanctions the suppression of opposition voices. The flawed election processes documented in 1996 continue today.

Human rights abuses. Extrajudicial killings, unwarranted incarcerations, kidnappings, disappearances – these are not historical relics but contemporary realities. Security forces use excessive force, at times resulting in death. Torture and other cruel treatment remain common.

Manipulation of the judiciary. Judicial processes and the rule of law are replaced by “rule by law” – the use of legal forms to achieve political ends. The international warrant for the Uganda Law Society president, Isaac Semakadke, now in self-imposed exile, exemplifies this pattern.

Manipulation of parliament. The legislature and its processes are bent to executive will. The national budget is skewed to favour the army and State House. The removal of presidential age limits and extension of term limits were accomplished through Parliament’s subordination.

Digital authoritarianism. Social media, the Internet and AI are devalued as tools for transforming Ugandan minds. The state monitors and controls digital spaces to favour political power retention and ‘perenniality’.

Intellectual repression. The state pursues de-politicisation, de-intellectualisation, and disempowerment. Public intellectualism and public scholarship are erased. Political education is banned in schools. Intellectual discourse and public-university interactions are discouraged.

Disciplinary education is perpetuated to narrow minds in the face of wicked problems. The sciences are separated with unprincipled preference for natural science and related professions. New and different knowledge production – team sciences – is rejected.

This is the full picture of constitutional decay. Military trials are one thread in this fabric—but they are a revealing thread, one that shows how the entire garment is woven.

Courage to be faithful

Chief Justice Owiny-Dollo insists that he needed no courage to decide the Kabaziguruka case. The law was clear. The Constitution was clear. A faithful judge had only to apply them.

This is true, but it is also too modest. In a system where faithfulness to law can carry personal and professional costs, the decision to be faithful is itself a form of courage – not the courage to defy the law, but the courage to obey it when obedience is costly.

The military trials controversy will continue. Parliament has passed its amendment. The courts will hear challenges. The president will defend his position. Civilians will continue to appear before military tribunals, and their lawyers will continue to object, and the slow grinding process of legal contestation will proceed.

But beneath the legal arguments, beneath the constitutional provisions and judicial precedents, lies a more fundamental question: What kind of country do Ugandans want to live in?

Do we want a country where law constrains power, or where power defines law? Do we want a country where citizens have rights that the state must respect, or where the state has powers that citizens must endure? Do we want a country where soldiers try civilians, or where civilians govern soldiers?

The Constitution of 1995 embodied answers to these questions. It declared that all power belongs to the people. It established institutions to ensure that power would be exercised accountably. It guaranteed rights that no government could abridge.

But a constitution is only paper until people defend it. The military trials controversy is one front in that defence. It will not be the last.

The question for Ugandans – for legislators, for judges, for lawyers, for activists, for ordinary citizens – is whether we have the courage to be faithful: faithful to the Constitution we gave ourselves, faithful to the rights it guarantees, faithful to the country it imagines.

If we do, the military courts will eventually be confined to their proper sphere: the discipline of soldiers, not the judgment of citizens. The Constitution will be restored. And the paper tiger of the 10-Point Programme will be replaced by something real: a government of laws, not men; of rights, not powers; of citizens, not subjects.

If we do not – if we accept military trials, legislative overrides, executive dominance, constitutional decay – then we will get the country we deserve: a country where power is all, law is nothing, and the gown devours its weaver.

The choice is ours. The time is now.

• A Tell Media report / By Oweyegha-Afunaduula. The writer is a retired Ugandan scholar and elder who has witnessed and analysed Uganda’s political evolution from colonialism through independence to the present day.