JUBA, South Sudan - In each country he used a different code name: He went by Charles as he traveled by road to Uganda and onto Congo; switched to Nathan as he flew to Rome; and then became Leonard when he picked up his fake passport and traveled to the Comoros Islands. It was only three weeks after setting out from dusty Juba, South Sudan - when he finally landed at his destination - that he heard his real name spoken out loud. "Welcome, Gen. Joseph Lagu," the Israeli officers receiving him at Ben-Gurion International Airport said. "We have been waiting for you."

The year was 1969, and the predominantly Christian and black southern Sudan was mired in a long and brutal civil war against the Muslim-Arab north, a war that would claim half a million casualties before a fragile truce was declared three years later. When the legendary South Sudanese commander returned home from his clandestine Israel mission that year, he carried with him Prime Minister Golda Meir's promise of weapons and training - critical help, he says today, that subsequently turned the south's struggle for freedom around. "It help set us on the path to where we are today," he says, "and that will never be forgotten."

"Today" is a week after Sudan's historic referendum, in which, after half a century of on-and-off civil war, the south overwhelmingly voted for independence, thus beginning the countdown to the birth of a new nation. Eighty-one years old and long retired, Gen. Lagu sits down for an afternoon tea in the shade of a dilapidated garden in Juba, the world's soon-to-be newest capital city, and talks about days gone by - and of a secret relationship few know about.

It all started with a personal letter, Lagu says, that he sent to Levi Eshkol after the Six-Day War. "Dear Prime Minister," Lagu wrote. "Congratulations for your victory against the Arabs. You are God Almighty's chosen people."

"One must always begin with a little flattery in these matters," he explains today, with a wink, as he places his wooden cane carefully upon his knees and nods to an assistant to pour the tea. "It was a good letter."

At the time, Lagu - one of the first people from southern Sudan to study at the prestigious military college in Omdurman, in the country's north (after which he received a commission to serve in the Sudanese army) and the very first, in 1963, to defect from the army and join the southern side in its civil war - was the founder and commander of the southern rebel movement known as the Anyanya, which means "snake venom" in Lagu's tribal Madi language. Among his junior officers in those days were John Garang, who later became leader of the southern rebels during the second civil war (1983-2005 ), and Salva Kiir, who took over the movement when Garang was killed in a helicopter crash in 2005, and is slated to be South Sudan's first president.

Lagu's counterpart at the time, the head of the movement's political wing, was a man named Joseph Oduho, and it was the late Oduho who introduced Lagu to the Israeli ambassador and political attache in Kampala, Uganda, where there was a growing Israeli presence in the late 1960s. "We have a common concern, and that is fighting the Arabs," Lagu wrote in the letter he gave the attache, asking him to pass it on up through the ranks.

The commander went on to offer a deal: If Israel would support Anyanya, Lagu promised to tie down the northern Sudanese armies so as to prevent them from joining the Egyptians and other Arabs from attacking Israel in the future.

"I waited for a response, but the problem was that Eshkol died. He never even saw that letter," says Lagu. "But luckily, he was followed by a woman who must have found that very letter and she contacted me. They were interested in the part where I said we would tie down the north, and believed we might even manage to tie up some of the Egyptian forces who would come to the north's assistance."

Golda Meir summoned Lagu to Israel, "practically smuggling him in," as he tells it. And during that first two-week trip to the country and the territories - in between tours to military bases around the country, from the Golan Heights to the Sinai and the West Bank - the Sudanese commander met with the prime minister in her Jerusalem office. They spoke about religion, and Lagu told her how, he recalls, "the Christian southerners considered Jews as the cousins of Christ." They talked arms. And then shook hands on a deal.

Short-lived relationship

Soon after, a shipment of weapons reached Juba from Israel - mainly two- and three-inch mortars, anti-tank missiles and light machine guns taken from enemy Arab countries during the 1967 war.

"They did not give us new weapons, or ones that were manufactured in Israel," Lagu explains, "as they did not want to be publicly known to be helping us."

Later, three Israeli advisors arrived and joined the rebels in the bush: a military advisor, a technician and a doctor. While other arms were coming in from Congolese rebels and international arms dealers, the Israeli assistance, Lagu explains, was what tipped the scales: "This helped transform my movement, and we became a force to be reckoned with. We began to make a real impact in the fighting against Khartoum."

The relationship with Israel might have been key, but it did not last for long. In 1972, Ugandan President Idi Amin, pressed by Egypt and Libya, did an about-face and turned against Israel, closing the embassy there and expelling all Israelis, including many military advisors. With this came an end to the use of Uganda as the main route for running arms to South Sudan - the other being an expensive airdrop into southern Sudan by planes flying over Ethiopia and refueling in Kenya.

Meanwhile, that same year, South and North Sudan signed the Addis Ababa Accords - a peace deal brokered by Ethiopia's Emperor Haile Selassie, in which the south promised to stop fighting in return for a great deal of religious and cultural autonomy. Khartoum insisted that all connection with the Israelis end immediately.

"Israel was somewhat upset by the peace deal," admits Lagu, who hurriedly went to Nairobi to explain the situation to his Israeli contacts. "But they understood we could not turn down peace. I needed to give my people a period of rest."

That rest lasted for 11 years, during which time the sides consolidated some of their military forces, and southern Sudanese ex-rebels, some of them trained by the Israelis, went north, a few of them even becoming instructors at the military academy there. "They had been trained well," he says.

The country, now suddenly made rich by the discovery of oil, also reunited politically to some extent, with Lagu himself taking on the role of vice president of Sudan.

But in 1983 civil war between north and south flared again - and this time Israel stayed away from the southern rebels. The reason for this, explains Lagu, was a secret deal between Sudanese President Gaafar Nimeiry and then-Defense Minister Ariel Sharon, arrived at even before the hostilities resumed.

"Nimeiry wanted to start fighting the south again, and get our oil and impose Islamic rule, but he knew he needed to neutralize the Israelis first," Lagu says. "So he called Sharon for a meeting in Nairobi, at which he told him that he accepted and respected the Camp David Accords and was now ready to be Israel's friend. But he then cautioned him and said: 'If Joseph Lagu or any of the southerners come to you in case of conflict - do not give them anything.'"

According to Lagu, Sharon then made a deal with the north - even though Khartoum was becoming increasingly fundamentalist under Nimeiry - and promised to shun the south in exchange for a promise of safe passage to Israel for Jews from Ethiopia through Sudan. "If we have your support, what do we need with Lagu?" Sharon reportedly told Nimeiry.

"After meeting Sharon, Nimeiry was confident and he became arrogant and said the Addis Ababa Accords were no longer viable. He then broke the treaty and ordered the use of force against southerners," Lagu recalls.

But, it turns out, Israel was not the only potential source of weapons for the south this time and, as the second civil war began in 1983, Libya's Muammar Gadhafi and Ethiopia's Mengistu Haile Mariam stepped in - each for his own political reasons - to help the rebels, now known as the Sudan People's Liberation Army, led by Lagu's old recruit Garang. "They armed the new movement with far better weapons than ever before and brought in military trainers from Germany. And now we had an even bigger war," says the old commander.

The second civil war went on for a full 22 years - the longest conflict in Africa - leaving two million dead and displacing a further four million. It featured a broadening of the conflict to other regions of Sudan, much in-fighting between the rebel factions themselves, and the involvement of a growing number of regional and international players: from Eritrea and Ethiopia, which went so far as to send in their own troops, to the United States and China, which each took and switched sides.

Significantly, the war also featured a growing number of weapons and military expertise, with everything and everyone from tanks and helicopters from the former Soviet Union to European mercenaries flooding the region.

In 2005, the two sides signed a comprehensive peace agreement, which held that the south would have autonomy for six years, followed by a referendum in which it would decide whether to break apart and create an independent nation, or remain as one. And it was this month, with that referendum, that the future was sealed.

"This has been a very long war," says Lagu, who today serves as a special advisor to Salva Kiir, his former officer and the man who is expected to be the first South Sudanese president. "And we are very close to what we hope is the very end."

Official results of the referendum are expected in early February, and if all goes according to plan, the split between North and South Sudan will formerly take place on July 9.

"We are leaving bitterness behind. If the north accepts us, we can accept them. We have grown old fighting," says Lagu.

As for Israel, he concludes, slowly draining his cold tea, he would like to make a return visit, even look up some of his old friends and visit the sites he once saw. And there is no reason why this will not happen.

"When we are independent, we will forge relations with whomever we want to," Lagu says. "And we still remember who our old friends are."

Future ties?

JUBA, South Sudan - "If it is in our national interest, we will do it," states Deng Alor, a rebel-fighter-turned-top-diplomat, who is slated to become South Sudan's first foreign minister come independence.

"No one will tell us what to do. Not the north, and not the Arab League," he tells Haaretz, sitting down for tea in an overly air-conditioned lobby of a hotel, as aides and bodyguards scurry around. "We struggled long and hard for the right to make our own decisions and we will not be hostage to any pressure."

A handsome man in his 50s - he is not exactly sure of his age - with a quick smile and a big gold watch, Alor, wearing a perfectly ironed white shirt, puts his three mobile phones on the table, and measures his words carefully. Even if, as widely anticipated, official results next week show South Sudan has voted to secede from the union, a transition period lies ahead before independence is declared on July 9.

During this period, South Sudan officially remains part of the Republic of Sudan. As such, officials here, including Alor, who until recently served as the republic's foreign minister, are not comfortable making announcements about future diplomatic plans that might go against existing law. Israel thus remains an enemy state in Sudan; it is prohibited to have any official ties or contact with the Jewish state.

Nonetheless, Juba is rife with speculation about the possible launch of diplomatic relations with Israel once independence is declared.

"No one will say it aloud, or on the record, but those relations will happen," says a senior official. "The north is always trying to discredit us, saying we get our weapons, even now, from Israel, when they know well this is untrue. So, better we keep quiet and not give them more reason to attack us. There is no need.

"If the north had not allowed for a peaceful referendum, we would have been released from the law and we could have turned to anyone we wanted in the international community to help us in a war. But as it happens, that was not the situation, so we must be patient."

As for the Arab League, the official says: "Let them not be hypocritical as some of them have relations themselves [with Israel]. Not to mention, we are not members of that league so who are they to dictate?"

"In the early days of our struggle, we had very good ties with Israel," is all Alor will allow himself to say. "And South Sudanese people have no historic problem with Israel whatsoever."

Speaking hypothetically, the future foreign minister adds that any relations forged in the future with Israel, or any other country, would, of course, include political, cultural, economic, civil-society and military exchanges.

"We would open all sectors," he says. "We need investment and development - this is our way forward."

Alor, who has traveled the world, has not been to Israel, but he does have some insider insight into the country: His niece has just returned with her three children after spending three years in Israel as an asylum seeker, and her husband remains there.

"She is facing some problems now," Alor says with a smile, "because her children only speak in Hebrew. There are not many Hebrew speakers in Juba. Not yet."