One reason for William Mackinnon's distraction from Indian business affairs after 1884–5 was the necessity of having to cope with a serious challenge to the future prospects of the Netherlands India S.N. Co (NISM) within the Indonesian archipelago. His great achievement in creating the Australasian United S.N. Co in 1886–7 meant that the Mackinnon group now dominated steamshipping in coastal waters throughout the great swathe of territory comprising India, Indonesia and Australia, and it had become the world's largest maritime conglomerate. However, pleasure in that accomplishment was short-lived, and much gloss taken off the triumph, by the fact that, even as the Australasian United S.N. Co came into being, events were already in train that would bring about the demise of the Netherlands India S.N. Co. Indonesian trade and shipping had served as a stepping-stone to Australia for William Mackinnon and his associates. Ironically, however, no sooner had the final stride in that direction been taken than the intermediary platform was whipped away from beneath them, leaving a yawning gap between their operations in South Asia and in Australia. The on-going integration of the deep-sea and shallow-water shipping activities of the four main companies within the Mackinnon group was swept away by a Dutch determination to exclude British shipping from their colonial possessions. The neomercantilist tendencies of the 1880s and 1890s – which saw European powers react to recurrent economic depression by raising levels of protection in home and colonial markets as well as by acquiring new colonial territories – threatened the activities of William Mackinnon and his business group at several points across their sprawling trade and transport empire. Nowhere, however, did they do so more centrally and more directly than in the Dutch East Indies.

In 1882, the immediate prospects of BI's ‘little sister’, the Netherlands India S.N. Co (NISM), appeared good. The company still had eight years to run in its contract with the government of the Netherlands Indies and a recent good run of financial results had enabled the payment of highly satisfactory dividends. NISM's success had its drawbacks – ‘the recent large dividends are encouraging competitors against us and for the same reason Govt. is trying to put everything on our shoulders that costs them money.’