The chapter opens with the statement: "The clock showed the time as 7:30 a.m." Clocks and time figure as prominent motifs in this chapter. Ishigami, reflecting upon the amount of time it would take to complete the math problem related to his senior's thesis, "calculates that it would take him roughly another twenty years to complete his work on this particular theory. Possibly even longer." Yukawa laments the fact that both he and Ishigami lead lives forever governed by the necessity of their synchronization with the clockwork of society: "too bad it's impossible for you and me to ever be off the clock. Like it or not, we are stuck in the cogs of society. Take them away, and are clocks spin out of control." Hearing this, Ishigami admonishes him for wasting time: "Keep chatting like this and you'll use up your two or three minutes in no time." The final words of the first section (i.e. "It's over") have a finality suggestive of one's time having run out. The presence of time as a constraining influence upon human freedom thus constitutes a central motif that organizes the first half of the chapter.

Ishigami's life is limited by time. He laments the fact that he can't dedicate himself fully to solving the math problem related to his senior's thesis. He views his own life quantitatively in terms of the amount of time required to perform various tasks. Hence, he notes the time when the chapter starts. He calculates the time needed to complete his senior thesis math problem. He chides Yukawa for wasting the time allocated for their conversation. Ishigami's entire life can be reduced to a temporal quantity that can be subdivided, allocated, wasted, or made use of. When Yukawa states, "You've got a precious brain and I don't want it being wasted like this," Ishigami responds, "I don't need you tell me that. I already abhor wasted time." It's no coincidence that Ishigami extends his sense of self as a time-dependent being to the homeless people whose routines he likens to "clockwork."

Since Ishigami is obsessed with numbers, mathematics, and time almost to the total exclusion of human feeling and compassion, Yukawa must use Ishigami's own metaphor of clockwork to convey the inherent value of human life. Hence, Yukawa goes out of his way to emphasize that "even a cog may say how it gets used." By speaking to Ishigami in a language that is comprehenible to him, Yukawa attempts to reprimand Ishigami for having taken his clockwork metaphor to such an extreme as to commit a horrible atrocity. It's noteworthy that Ishigami's morning commute follows the same pattern as in Chapter 1, echoing the prose and language of that chapter, except for the notable absence of the "Engineer," who is no longer to be found sitting on his usual bench. This absence, as we will find out, is the doing of Ishigami himself and the result of his mathematical and quantitative worldview taken to an extreme. It's for this reason that Yukawa attempts to remedy Ishigami's lack of remorse by couching his language in terms that Ishigami can understand.

Yukawa does not take a judgmental attitude towards Ishigami in spite of his realization that Ishigami has committed a morally repulsive deed. In fact, Yukawa emphasizes the fact that he is talking to Ishigami strictly as a friend who has Ishigami's interests at heart and who doesn't wish to see Ishigami's life wasted. Whereas any other person would react with visceral horror upon learning of the full extent of Ishigami's apparent callousness, Yukawa, being the scientist that he is, views people from a logical point of view that enables him to understand them and thereby feel a measure of compassion for them at the same time.

Finally, Yukawa indicates that he's solved the question of whether or not it's easier to create a problem or to solve the same problem yourself. The answer is the latter - so long as one can understand the person who develops the problem. This is a solution that involves empathy and compassion rather than abstract proofs in which the human beings proposing and solving the problems in question aren't taken into account. In this way, Yukawa conveys the idea that many complex mathematical problems cannot be solved solely on the basis of math and logic alone. They require a consideration for the concrete human element that is not taken into account in abstract reasoning.