During the late-19th century, Africa was rapidly being claimed and exploited by European colonial powers. After the 1885 Berlin Conference regarding West Africa, Europe's great powers went after any remaining lands in Africa that were not already under another European nation's influence. This period in African history is usually called the Scramble for Africa. The two principal powers involved in this scramble were Britain and France, along with Germany, Belgium, Italy, Portugal, and Spain.
The French thrust into the African interior was mainly from the continent's Atlantic coast (modern Senegal) eastward, through the Sahel along the southern border of the Sahara, a territory covering modern Senegal, Mali, Niger, and Chad. Their ultimate goal was to have an uninterrupted link between the Niger River and the Nile, hence controlling all trade to and from the Sahel region, by virtue of their existing control over the caravan routes through the Sahara. France also had an outpost near the mouth of the Red Sea in Djibouti (French Somaliland), which could serve as an eastern anchor to an east-west belt of French territory across the continent.
The British, on the other hand, wanted to link their possessions in Southern Africa (South Africa, Bechuanaland and Rhodesia), with their territories in East Africa (modern Kenya), and these two areas with the Nile basin. Sudan, which then included today's South Sudan and Uganda, was the key to the fulfilment of these ambitions, especially since Egypt was already under British control. This 'red line' (i.e. a proposed railway, see Cape to Cairo Railway) through Africa was made most famous by the British and South African political force Cecil Rhodes, who wanted Africa "painted [British] Red".
If one draws a line from Cape Town to Cairo (Rhodes' dream) and another line from Dakar to French Somaliland (now Djibouti) by the Red Sea in the Horn (the French ambition), these two lines intersect in eastern South Sudan near the town of Fashoda (present-day Kodok), explaining its strategic importance. The French east-west axis and the British north-south axis could not co-exist; the nation that could occupy and hold the crossing of the two axes would be the only one able to proceed with its plan.
Fashoda was also bound up in the Egyptian Question, a long running dispute between the United Kingdom and France over the legality of the British occupation of Egypt. Since 1882 many French politicians, particularly those of the parti colonial, had come to regret France’s decision not to join with Britain in occupying the country. They hoped to force Britain to leave, and thought that a colonial outpost on the Upper Nile could serve as a base for French gunboats. These in turn were expected to make the British abandon Egypt. Another proposed scheme involved a massive dam, cutting off the Nile’s water supply and forcing the British out. These ideas were highly impractical, but they succeeded in alarming many British officials.