Ibadan had already become involved in yet another war over trade with Egba and Ijebu in 1877, when Ibadan traders on their way from Porto Novo with firearms were attacked by the Egba. This gave the Ekiti and the Ijesa their chance. In 1878, the revolt against Ibadan rule started with the massacre of Ibadan officials in Ijesa, Igbomina and Ekiti. This led to a war which dragged on for sixteen years. Eventually, Ibadan found itself fighting on five fronts. In the east it faced the Ekitiparapo under the command of Ogedemgbe, the Seriki of Ijesa. In the south it faced the Egba and Ijebu. Ilorin joined in in the north. Finally, Ife joined the alliance in 1882. There had long been friction between the Ife and the Oyo settlers at Modakeke. These animosities were strengthened by the war during which Ife itself was sacked by the Modakeke and their Ibadan allies, and Modakeke was sacked by the Ife and Ekiti.

The main action of the war, however, took place in the north-east. The Ibadan and Ekitiparapo forces faced each other at Kiriji, a few miles east of Ikirun. Control of the trade routes was a major issue. There were three main routes to the interior, via Egba, Ijebu and Ondo. The Ondo route had been opened up by the British because of the frequent closure of the other roads. During this war, it became the main supply route for both sides (Akintoye, 1969). Some Ibadan supplies were able to get through via Ijebu. The war was unpopular with Ijebu traders, and the Awujale was forced into exile in 1885. Despite this, the flow of supplies was not completely free. Ijebu traders' profit margins were high, and they retained strict control of trade through the kingdom (Johnson, 1921: 610-11).

After some initial reverses, the Ekitiparapo gained something of an advantage in the conflict, and the help they received from Ekiti Saro merchants in Lagos was crucial. The most important factor was the supply of breech-loading rifles, much more accurate than the arms being used by the rest of the Yoruba, though the Ibadan were later able to get a small supply of them as well (Akintoye, 1971: 119).

Attempts at mediation had started as early as 1879-80. Both the Alafin and the Oni were involved, but neither was trusted by both sides, and Ife later joined in the fighting. The Lagos government was under instructions from London and Accra to keep out of the conflict, even though the fighting was having serious effects on the economic life of the colony. Under commercial and mission pressure, the Lagos government attempted to mediate but was rebuffed, and from 1882 to 1884 the British did nothing. Attempts by Saro in Lagos and by the Fulani emirs to end the conflict also failed.

After 1885 the attitude of the administration started to change. Firstly, there was the changing political status of Lagos which was separated from the Gold Coast in 1886. Secondly, the scramble for Africa by the colonial powers was well under way, and there were fears of French interference. Thirdly, some of the main protagonists of the war were themselves getting tired of it (Akintoye, 1971: 176).

To negotiate a peace, the administration turned to the CMS. A ceasefire was arranged in 1886 through the efforts of Samuel Johnson, the historian, and Charles Phillips, later the Bishop of Ondo. The parties then signed a treaty in Lagos with Governor Maloney which provided for the independence of the Ekitiparapo towns and the evacuation of Modakeke, to suit Ife,. This proved impossible to carry out. Ilorin refused to stop fighting in the north where it was besieging Ofa. Thus the war dragged on, and the forces refused to disband (Akintoye, 1971: 181-4).

British fears of the French soon appeared justified. There was the curious incident of 1888 when an employee of a French company persuaded the Egba chiefs to sign a treaty with France, providing for the construction of a rail link with Porto Novo (Ayandele, 1966: 49-51). This was a direct threat to trade with Lagos, but the French refused to ratify the treaty. The two powers hastily agreed on a frontier in 1889 (Anene, 1963). The areas recently invaded by Dahomey fell within the French sphere of influence. The British moved into the interior with the establishment of a post at Ilaro in 1890, while the French invaded Dahomey in 1892.

More aggressive measures to extend British control in the interior came with the arrival of Governor Carter in 1891. Like Glover, he took the view that the key to the situation lay in control of the trade routes through Ijebu and Egba. The result was the Ijebu expedition of 1892 (Ayandele, 1966: 54-69; Smith, 1971b). Ayandele suggests that in fact the Ijebu had showed more willingness to open the road than the Egba, but the decision to attack Ijebu was based partly on the hostility of the missions: unlike Egba, Ijebu had never allowed them in. The impact of the expedition was considerable. In 1893, Carter was able to set off on a tour around Yorubaland, making treaties with Oyo and Egba, and finally persuading the Ibadan and Ekitiparapo forces to disperse. The Egba opened the road to Ibadan, and allowed the start of railway construction. After two final incidents, the bombardment of Oyo in 1895 (Ayandele, 1967) and the capture of Ilorin by the Royal Niger Company in 1897, effective colonial control was established throughout most of Yorubaland.