How does Heart of Darkness cast doubt on European civilization's ethical certainties?
The idea of Imperialism was to spread European civilization to far and exotic places; this would allow outposts and military camps for strategic intelligence, as well as allowing the import of expensive goods without the trouble of dealing with native peoples. Kurtz represents the worst of that thinking, allowing his ability to influence and control the natives to give him delusions of grandeur; he is unable to separate his job from his need to control, and so even as he exerts his influence on the jungle, it destroys him from the inside. The ethical certainty of Imperialism that native peoples needed to be "saved" or remade in European image fails because of Kurtz's selfishness and his madness.
Marlow has a similar epiphany, but is saved by his fundamental decency; he views the natives with disdain, as all Europeans did at the time, but also allows them their humanity. For instance, when he views a line of prisoners, he thinks:
They passed me within six inches, without a glance, with that complete, deathlike indifference of unhappy savages. Behind this raw matter one of the reclaimed, the product of the new forces at work, strolled despondently, carrying a rifle by its middle.
(Conrad, Heart of Darkness, eNotes eText)
His view is typical of the time, as native people were seen as child-like, able to be "reclaimed" and formed into almost a parody of accepted, civilized norms. However, through this patina of indred racism, he tries to make his small piece of the world better, not worse, and so he represents the best ideals of Imperialism; his survival contrasts with Kurtz's death because while the missions slowly failed and withdrew, the ideals remained alive for years after.
Conrad's novel takes place during the European Age of Imperialism. European countries were expanding into all areas of the globe, claiming territories that were inhabited by undeveloped, "savage" populations. One of the justifications of this quest for more land and resources was touted to be the betterment of the native populations in the area. Poems like Rudyard Kipling's "The White Man's Burden" reflect a belief among civilized Europeans of the time that they were bound by a mission to help mankind -- a mission to "civilize" the indigenous natives of these remote, newly conquered lands.
In "Heart of Darkness," Joseph Conrad reveals, through Marlowe's eyes, the true purposes of the Company, as he calls it. Purposes of stripping the land of valuable ivory, subduing and enslaving the native population for selfish gain, and leaving the land and its peoples in a state of devastation and disarray. Marlowe's recounting of his experience reveals the false idea of the European as, "Something like an emissary of light, something like a lower sort of apostle." Marlowe's aunt expresses these popular notions among her civilized friends, telling them that her nephew is going to, "[wean] those ignorant millions from their horrid ways."
No doubt Marlowe's aunt reflects the moral swag that dominated European mindsets of the time. They believed they were bettering less fortunate and less intelligible beings by developing their lands and teaching them how to be civilized. However, this notion comes into sharp contrast with what Marlowe actually observes when he arrives at the Outer Station in the Congo. What he relates is a virtual demolition zone, with destruction, death and decay on every side. He watches groups of the abused natives crawling into shadowed groves to die from their mistreatment. The further he goes inland, the more damage and loss he observes. Finally after reaching Kurtz's inner station, he finds the completed corruption of that European mindset. Kurtz abused his power over the natives in order to ravage the land of ivory. This is epitomized by the native heads posted on spikes about Kurtz's hut. Kurtz, the European "savior", the Company's pride, is in reality a delusional, deranged, greedy, and violent murderer - a true savage. The natives, in contrast, are portrayed as merely pawns in a European money game.
It is significant to note that Conrad specifically portrays the Belgian holdings in the Congo by King Leopold II. Conrad focuses his perspectives on the false notions of the incoming Europeans, not on racial inequality, though Marlowe's horror at what he observes would indicate a valid concern. I have added a link below that shows the theme of deception woven throughout "Heart of Darkness."