At 3:30 a.m. on Thursday, Bashir was visited by the heads of his four main security apparatuses and was told “there was no alternative” but for him to step down, two senior military sources with direct knowledge of the conversation told CNN. According to the sources, Bashir responded by saying “with the blessings of God,” an expression of acquiescence in Islamic tradition. His personal guard has been replaced and is under close watch, according to sources. The Sudanese Prime Minister Mohamed, Taher Ayala, and the head of the ruling National Congress Party, Ahmed Haroun, were among dozens of officials who were also arrested, a top military official with direct knowledge of the arrests told CNN. CNN’s stringer in Khartoum witnessed military troops storming the Islamic Movement headquarters, the main component of the ruling party. Read MoreReports of Bashir’s ouster come amid a popular uprising against his rule that has seen thousands take to the streets across the country. The largely peaceful protests have escalated in recent days, as different armed government groups engaged in deadly clashes. The Sudanese Intelligence Agency said it ordered the release of all political detainees, the official news agency (SUNA) reported on Thursday. More than 3,000 people have been arrested since protests began in December, based on testimony gathered by CNN from activists, lawyers and victims. The Sudanese army will deliver a “statement shortly,” Sudan state TV announced on Thursday morning. As news of Bashir’s removal spread, people flooded the streets in Khartoum in celebration, according to social media reports and witnesses on the ground. Sudanese demonstrators on Thursday cheer as they attend a protest rally demanding Sudanese President Omar Al-Bashir to step down outside the Defence Ministry in Khartoum.Thousands marched towards Khartoum’s military headquarters, dancing, banging drums and chanting against the government. Cars honked their horns in support and women ululated in celebration.”He is a coward and he has fallen!” people were heard chanting amid an extensive military presence on the streets of the capital. The country’s Rapid Security Forces, seen as close to Bashir, were widespread and did not engage with the crowds. Military troops were seen celebrating with protesters, flashing victory signs. One soldier was seen patting a protester’s back and congratulating him. Photos: In pictures: Sudanese protest three-decade rule of President al-BashirSudanese demonstrators cheer as they attend a protest rally demanding Sudanese President Omar al-Bashir step down, outside the Defence Ministry in Khartoum, Sudan, on Thursday, April 11.Hide Caption 1 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirDemonstrators rally demanding Bashir’s removal from office on Wednesday, April 10.Hide Caption 2 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirAlaa Salah, a Sudanese woman propelled to internet fame earlier this week after clips of her leading powerful protest chants against Bashir went viral, addresses protesters during a demonstration in front of the military headquarters on Wednesday, April 10.Hide Caption 3 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirSudanese protesters salute a military armored vehicle on Tuesday, April 9.Hide Caption 4 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirSudanese soldiers transport a body covered in cloth in a pickup truck near the military headquarters on Tuesday, April 9.Hide Caption 5 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirA person writes “Down with Bashir” as demonstrators take part in a protest demanding the departure of Bashir on Tuesday, April 9.Hide Caption 6 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirA demonstration is held on Monday, April 8.Hide Caption 7 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirA protester shows bullet cartridges as others gather in front of security forces during a demonstration on April 8.Hide Caption 8 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirProtesters sit atop a military vehicle next to soldiers on Sunday, April 7, as they rallied for a second day urging the military to back them.Hide Caption 9 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirDemonstrators pray outside the military headquarters on Sunday, April 7.Hide Caption 10 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirProtesters gather for a rally on Sunday, April 7.Hide Caption 11 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirA demonstrator waves the national flag on Sunday, April7.Hide Caption 12 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirProtesters run for cover as tear gas canisters are fired by police on Saturday, April 6.Hide Caption 13 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirA Sudanese protester retreats from tear gas during an anti-government demonstration in Khartoum’s district of Burri on February 24.Hide Caption 14 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirA Sudanese protester carries a portrait of Bashir with Arabic writing that reads “down and that is all” during a demonstration on February 8.Hide Caption 15 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirSudanese protesters take part in an anti-government demonstration in Omdurman, Sudan, on Tuesday, January 29.Hide Caption 16 of 17 Photos: In pictures: Sudanese protest three-decade rule of President al-BashirA protester is seen in the midst of tear gas during clashes with security forces in Khartoum on December 21, 2018.Hide Caption 17 of 17But a group that has been leading the protests, the Sudanese Professionals Association, has called on people to press on with demonstrations, and to stage a sit-in outside military headquarters. In a statement provided to CNN, the umbrella organization of doctors, lawyers and journalists warned against exclusive military rule.”What we do not accept is to reproduce the regime for itself, or that the army will be solo in power,” said the SPA. In its Declaration of Freedom and Change, the SPA lists the toppling of the regime and the handover of power to a transitional civilian national government among its list of demands.In a separate public statement addressing protesters, Thursday, the SPA said they will protect the “revolution until all its goals are completely achieved.” Bashir took control after a coup in 1989 and became President in 1993. He stands accused of conducting a campaign of ethnic cleansing in the country’s Darfur region, and was nearly arrested in 2015 while visiting South Africa. He faces five counts of crimes against humanity and two counts of war crimes in connection to Sudanese military actions in Darfur.The International Criminal Court has issued two arrest warrants for him, and considers him to be “at large.”In this July 9, 2018, file photo, Sudan’s President Omar al-Bashir attends a ceremony for Turkish President Recep Tayyip Erdogan at the Presidential Palace in Ankara, Turkey. The protesters started as a demonstration against the rising costs of living but escalated into a push for the Bashir’s removal from office, with mass rallies and sit-ins outside the presidential compound and army headquarters. In February, Bashir declared a year-long state of emergency in response to the protests. This week’s sit-in had grown into one of the biggest rallies since the uprising began earlier this year, with crowds braving temperatures of more than 110 degrees Fahrenheit (43 degrees Celsius) to camp out in the streets of the capital.On Tuesday, members of the Sudanese army moved in to protect protesters in Khartoum, after national security forces attempted to break up the third day of a mass sit-ins.Earlier in the week, the mood among protesters outside the compound had verged on victorious, with people chanting “thawra” (revolution) and waving the national flag aloft as soldiers looked on, footage from the scene showed.This woman has come to symbolize Sudan's protestsPhotos captured protesters sitting atop military vehicles and handing out water bottles, as others posed for selfies with members of the armed forces, flashing V-for-victory gestures.A CNN team visited the capital of Khartoum undercover last month, where they heard reports of possible war crimes by security forces attempting to quell the demonstrations.Sudanese protesters cheer for passing soldiers near the military headquarters in the capital Khartoum on April 11, 2019The Central Committee of Sudan Doctors said 22 people, including five soldiers, were killed in mass protests since Saturday. Sudan’s government has reported some 32 fatalities since the protests began earlier this year, including three security personnel, but doctors and opposition activists suggest the toll is 78, excluding the military. Sudan has sought to censor news coverage of protests, and journalists found reporting on the demonstrations risk life imprisonment and the death penalty.