The premise of this article is that you want to cross Africa, from north to south, overland. The traditional way of doing this was to take the 'S route' from Morocco downwards, and thereby to avoid both south Egypt and Sudan, and also the various options that presented themselves to you from there.
Using the 'S route', you would cross from Morocco to Western Sahara and then Mauritania, and then you would turn east and head through the various countries of West Africa until you got to Cameroon. From there you would enter the Central African Republic, and then traverse northeastern DRC (via Kisangani, a city in northeastern DRC) until you reached Uganda. From Uganda the journey is as follows:
However this route became closed several years ago due to civil war and extremely violent military instability in the Central African Republic. Hence people started re-exploring a direct route down from Egypt to Uganda, which is now passable and has remained so for several years. The route is Egypt-Sudan-Ethiopia-Uganda, and then on as before. Here we describe how to do it.
We describe the route by public transport, but many people choose to drive it instead in their private vehicles. Of course driving assumes an extremely rugged vehicle and involves purchasing lots of different insurance policies at different borders, and also involves endless police stops in some countries as they try to gouge you.
So here is the public transport route.
Egypt to Sudan
We assume you start on Egypt's Mediterranean coast, and her northernmost city Alexandria (known locally as Iliskindrya). From Alexandria to Cairo there is a perfectly respectable train that runs several times a day and takes two and a half hours (although it is usually late).
Alexandria
If you need to stay overnight in Cairo - or just take a hotel for a few hours - there are plenty of extremely nasty hotels round the back of the railway station. Take a nasty hotel near the station rather than a decent one further away, because the traffic in driving to and from Cairo Ramses railway station is horrendous like nothing you have seen before. Many a train has been missed in a taxi waiting in traffic heading to or from the railway station.
Traffic in the vicinity of Cairo railway station
There is a daily train at about 22h00 (check the exact time but it is usually late departing) to Aswan, the southernmost city in Egypt. In theory the journey takes 15 hours but in practice the train is late departing and even later arriving. It is a grimy train and do not think of travelling other than in first class. Even that is not going to be pleasant. This is an African train.
Cairo Ramses Railway Station
These photos are grossly over-glamorous
The next step is to take the ferry down Lake Nasser from Aswan (it has a port) to Wadi Halfa, the first town in northern Sudan. This ferry goes once a week and takes about 18 hours. It's a rough business. It's quite hard to work out which day the ferry goes from Aswan until you're in Aswan. Therefore be prepared to wait a few days in Aswan in a hotel with air conditioning, particularly in summer. (Aswan is blisteringly hot.)
The Sofitel in Aswan. Most of Aswan does not look quite like this; but if you can afford it, this is the last decent hotel you will find before Addis Ababa
You can also drive from Aswan to Wadi Halfa. It takes a good 30 hours through the desert. You might be able to find a bus in Aswan that will take even longer and be even more hellish. The ferry is the way to go. (The ferry also takes cars but we dread to imagine what the bureaucracy involved in that is like.)
Aswan ferry
You must have your Sudanese visa before you board the ferry. Although there is a Sudanese consult in Aswan that in theory issues visas, it is contra-indicated. You are better off applying in Cairo. You will need an invitation to obtain a Sudanese visa; various dubious agencies in Cairo can arrange this for you if you arrive in Cairo without a Sudanese visa.
The best description we have found of how to apply for a Sudanese visa in Egypt (an inevitably painful process) is here:
Sudan to Ethiopia
Once you arrive in Wadi Halfa port, it is about 5km through the desert to get to Wadi Halfa town. Have water with you. Do not assume there will be anyone to give you a ride, although you might be lucky.
Wadi Halfa is very hot. Pause on these words to consider what they mean. You have never been anywhere so hot. The mean daily maximum temperature in summer is 52 centigrade. It doesn't drop much at nights, and we are not aware of any building in Wadi Halfa with functional air conditioning. 'Cold' water comes out of the taps so hot it is almost too hot to hold your hands under. You'll be having a lovely time in Wadi Halfa, where you may well spend several days, waiting for onward transport. It's full of sights for the tourist: sand dunes; desert rocks; sand roads, etcetera.
Wadi Halfa
Wadi Halfa has a notoriously bad hotel where you can stay pending the train from Wadi Halfa to Khartoum. We can describe that train is no better terms than this:
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Every third Tuesday a train allegedly leaves Wadi Halfa at 17:40, arriving Atbara on Wednesday evening and Khartoum (Bahri station in the north) on Thursday morning.
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This train is very bad. Only travel first class. Expect to be covered in sand and dirt within the first half an hour, and not to get much sleep. Also expect it to be late. Very late (e.g. 18-24 hours).
Train from Wadi Halfa to Khartoum
There are also various buses from Wadi Halfa to Khartoum. They seem to exhibit no regularity and they will probably take 24-36 hours. They will be much more ghastly than the train.
Typical Sudanese or Ethiopian bus. Obvious note: dangerous and dirty
Welcome to Khartoum. After all this, spend a couple of nights in a decent hotel (Khartoum is ghastly) but note that Khartoum is dry. There is no liquor. Although quieter than Cairo, Khartoum is hellishly hot (common theme in the region) and with no redeeming features whatsoever. Stay away from the Police and other officials. They will bleed you for every last penny you have.
Khartoum
From Khartoum to Addis Ababa, the capital of Ethiopia, is over 24 hours by one or more buses heading southeast from Khartoum. You might pick up a 'technical' (a jeep with no roof over the back, where you sit or stand) if you are lucky, for some or all of the way. Take a technical if you can. The buses are typically Ethiopian - wooden benches on trucks.
A 'technical'
Expect the border to be arduous. Every official is thoroughly bloody minded in this part of the world. It is highly preferable to arrive at the border with an Ethiopian visa. The Addis Ababa airport 'visa on arrival' system is highly likely not to work at Ethiopia's land borders. And then you will be f++ked.
Scene from near the Sudan / Ethiopia border
Sudan to South Sudan
We mention this solely to counsel you against it. There are no roads from Khartoum to Juba (the capital of South Sudan). If you're lucky, it's about 36 hours on a technical through mud and fields with the vehicle on wooden river rafts. If you're unlucky, your driver gets lost or the river raft sinks and you die.
Typical obstacle on the drive from Khartoum to Juba
Make sure you satisfy South Sudanese visa requirements well before you get this far.
Typical transport traversing the border between Sudan and South Sudan
If you do make it to Juba, it is about 12 hours further by bus to Kampala on a gravel / mud road. Note that Juba has nothing really approximating to tourist hotels or any other infrastructure. You'll end up overnighting there by doing something silly, such as sleeping in a cow shed - full of cows. You will be thoroughly ill so take all conceivable medications.
Downtown Juba
Do not believe images like this of Juba. Juba is very rough
One of the better stretches of road south of Juba
Ethiopia to Uganda
Addis Ababa is filthy, dangerous and confusing so unless you stay in its top five-star hotel, you will want to be moving on pretty quickly.
Addis Ababa
Addis Ababa to Kampala is about 48 hours on an Ethiopian bus (the sort with wooden benches in the back of a truck). All Ethiopian roads are terrible; Ugandan ones are fine.
Ethiopian road
Uganda onwards
Kampala itself is safe, with moderate weather, although cramped and overcrowded.
Kampala
The map at the top of this essay shows you the onward route to take from Kampala to get to South Africa. This part is all much easier than what we describe here, which is a nightmare and living hell and inevitably takes a few weeks.
Good luck!