[guided]The diagonal machine must do two jobs at once. First, it must identify which machine it is diagonalizing against. That is the role of the code $\langle M\rangle$. Second, it must defeat not just machines running in at most $t(n)$ steps, but machines running in at most $c\,t(n)$ steps for an arbitrary constant $c > 0$. That is why the input includes the unary integer $a$: later, when a particular alleged decider has running time bounded by $c\,t(n)$, we choose $a > c$.
Formally, on input $w \in \{0,1\}^*$ with length $n := |w|$, the machine $D$ first parses $w$. If the parsing fails, $D$ rejects. If the parsing succeeds, then
\begin{align*}
w = \langle M\rangle \# 1^a \# z
\end{align*}
for a deterministic Turing machine $M$, an integer $a \in \mathbb{N}$, and padding $z \in \{0,1\}^*$. The machine $D$ then invokes the clock for $t$ on length $n$. Time-constructibility is exactly the hypothesis that lets $D$ enforce a cutoff depending on $t(n)$ by deterministic computation.
The simulation cutoff is the value of the already defined map $S: D_{\mathrm{in}} \to \mathbb{N}$ at $w$, namely
\begin{align*}
S(w) = a\,t(n).
\end{align*}
If the clock machine is given in the exact-time form, $D$ does not need to write $t(n)$ in binary. It runs $a$ clock phases, each lasting exactly $t(n)$ steps, and advances the simulation of $M$ on $w$ by one simulated step during each clock step. This permits exactly $a\,t(n)$ simulated steps. The machine $D$ simulates $M$ on the identical input $w$ for at most $S(w)$ simulated steps. If $M$ accepts within the cutoff, $D$ rejects; if $M$ rejects within the cutoff, $D$ accepts; and if $M$ does not halt within the cutoff, $D$ rejects. Thus the only time $D$ accepts is when the encoded machine definitely rejects its own diagonal input within the allotted time.
This is the diagonal flip: whenever $M$ is given enough simulated time to exhibit its answer on $w$, the machine $D$ returns the opposite answer.[/guided]