Siddhartha is speaking to Gotama, the Buddha. In chapter three, titled "Gotama," Siddhartha and Govinda have left the samanas to investigate the rumors of Gotama the Buddha because "he had reached Nirvana and would not return time and again to the circle of existence, he did not submerge himself any longer in the turbulent streams of mortal beings" (10).
Govinda remained behind with Gotama Buddha while Siddhartha traveled on, still searching. Before he left, he spoke with Gotama. The quoted section in your question is part of that conversation.
Siddhartha is saying to the Buddha that according to his very own teachings everything in the world is a perfect chain of cause and effect. Everything is connected. BUT this perfect chain of cause and effect is broken in one place and that break is the Buddha. He broke free of the "chain" of causation, of cause and effect. He is no longer a part of the circle of existence, and THAT can't be explained.
Ultimately Siddhartha's objection to the Buddha is that he won't ever be able to teach anyone to reach nirvana - to do what HE did. Siddhartha is (at this time in his own life) objecting to any kind of teaching for this very reason. He feels that the only way that he will understand the eternal atman in him (atman in the novel - roughly equivalent to the soul in Christian culture) is to learn from himself. He cannot learn himself from another teacher.
Buddha's response is that his teachings are not trying to "explain the world to those who seek knowledge. They have a different goal; their goal is salvation from suffering. This is that which Gotama
teaches, and nothing else" (15). Gotama Buddha tells him that he's not teaching nirvana; he's teaching salvation from suffering.