The Sudan crisis could become a major contagion in the region's security and trade and also escalate the divisions in the Gulf Peninsula manifested in the current war in Yemen.
Already, countries like Chad, South Sudan and Eritrea are feeling the impact of insecurity, while countries like Kenya are worried about their lucrative tea trade, and Ethiopia is concerned about the stalled tripartite negotiations on the Nile waters.
For Chad, the ongoing crisis has affected the security co-operation with the Sudanese government that was struck between ousted president Omar al-Bashir and President Idriss Déby, to eliminate the Union of Resistance Forces (URF) based in the northeast.
In Darfur, the Sudan Liberation Movement (SLM) and the Justice and Equality Movement (JEM) armed groups have been waiting on the side-lines as the crisis unfolds and as they are mainly excluded in the negotiations for the transition to civilian rule.
Biel Boutrous Biel, the executive director, the South Sudan Human Rights Society for Advocacy said besides the obvious implications of Bashir's departure for the South Sudan peace deal, there is a danger that rebels in Darfur, Southern Kordofan and Blue Nile could take advantage of the vacuum to push for secession.
"These are tough times that will redefine the politics of both Sudan and South Sudan. For instance, Dr Riek Machar and other South Sudanese opposition leaders, who were depending on Sudan's mediation, will have to think of new strategies to fit in the merging political dynamics in the Sudan. Otherwise, things will be hard for peace in South Sudan," said Mr Biel.
At last count, about 13 rebel or political movements were active in Sudan, most of them at the border regions and pitting expatriate Arabs, Sudanese Arabs, camel keepers, cattle keepers and sedentary farmers against each other.
They have backing from neighbouring countries like Ethiopia, Chad, Libya, Eritrea and far away financiers like Kuwait, Turkey, United Arab Emirates, Iran, Qatar and Saudi Arabia. Abyei and Darfur host most of the rebel groups with the possible exception of Rashaida Free Lions and Beja Congress to the east.
For South Sudan, apart from the uncertainty of the smooth importation of food and manufactured goods, increased insecurity in the Blue Nile and Southern Kordofan regions is a threat to its efforts to control proliferation of arms.
Since the crisis began in December 2018, there has been resumption of significant clashes across the Jebel Marra region of Darfur between government forces and the Sudan Liberation Army led by Abdul Wahid.
A United Nations report released in February expressed concern that the Sudan crisis plus instability in neighbouring Libya remains a major source of possible conflict spill over in the region, including Darfur.
In Kenya, the crisis forced the cancellation of the national carrier's daily flights to Khartoum that are essential for business and to Kenyan tea exports to Sudan, its fourth largest market outlet that accounts for up to 10 per cent of Kenyan tea exports and also as an entry point to the Libyan, Central African Republic and Cameroonian markets.
In Ethiopia, Prime Minister Abiy Ahmed Ali is trying to mediate between Sudan's ruling Transitional Military Council and the protesters because Addis Ababa is not only worried about increased insecurity in the bordering Blue Nile State, but also because Sudan is its key partner in the negotiations with Egypt over the use of the Nile waters.
But the biggest challenge comes from across the Red Sea. Analysts warn that Sudan is likely to be a major theatre for proxy wars between Saudi Arabia and the United Arab Emirates on one hand and Qatar, Turkey and Iran on the other.
On June 8, the Mo Ibrahim Foundation released a letter accusing some regional powers, led by Saudi Arabia, of appearing to side with the military.
"China is damaging its standing and its reputation in Africa by blocking the UN Security Council resolution condemning the military council's violence. We have not seen a single tweet from the White House in support of the people of Sudan and of democracy," says the letter.
The resolution, blocked by China and Russia, has however since been passed, calling for no attacks on civilians and upholding of human rights.
The US this week also named Donald Booth special envoy to Sudan with the mandate of finding a peaceful political solution between the two sides.