[proofplan]
We construct the inverse map explicitly. Starting from an element $u \in F(A)$, we define a natural transformation $\alpha_u: H_A \to F$ by sending a morphism $f: A \to X$ to $F(f)(u) \in F(X)$. Functoriality of $F$ proves naturality, and the two inverse identities follow from evaluating at $\operatorname{id}_A$ and from the naturality square for an arbitrary natural transformation.
[/proofplan]
[step:Construct a natural transformation from an element of $F(A)$]
Let $u \in F(A)$. For each object $X \in \operatorname{Ob}(\mathcal C)$, define a function
\begin{align*}
(\alpha_u)_X: \operatorname{Hom}_{\mathcal C}(A,X) &\to F(X) \\
f &\mapsto F(f)(u).
\end{align*}
Here $f: A \to X$ is a morphism in $\mathcal C$, so $F(f): F(A) \to F(X)$ is a function because $F$ is a covariant functor.
We verify that the family $\alpha_u = ((\alpha_u)_X)_{X \in \operatorname{Ob}(\mathcal C)}$ is natural. Let $g: X \to Y$ be a morphism in $\mathcal C$, and let $f \in \operatorname{Hom}_{\mathcal C}(A,X)$. The hom-functor $H_A$ sends $g$ to the function $H_A(g): \operatorname{Hom}_{\mathcal C}(A,X) \to \operatorname{Hom}_{\mathcal C}(A,Y)$ given by $H_A(g)(f)=g \circ f$. Therefore
\begin{align*}
F(g)\bigl((\alpha_u)_X(f)\bigr)
&= F(g)\bigl(F(f)(u)\bigr) \\
&= (F(g) \circ F(f))(u) \\
&= F(g \circ f)(u) \\
&= (\alpha_u)_Y(g \circ f) \\
&= (\alpha_u)_Y\bigl(H_A(g)(f)\bigr).
\end{align*}
The third equality is functoriality of $F$. Hence
\begin{align*}
F(g) \circ (\alpha_u)_X = (\alpha_u)_Y \circ H_A(g),
\end{align*}
so $\alpha_u: H_A \to F$ is a natural transformation. Define
\begin{align*}
\Psi: F(A) &\to \operatorname{Nat}(H_A,F) \\
u &\mapsto \alpha_u.
\end{align*}
[guided]
We want to reverse the evaluation map $\Theta$. If an element $u \in F(A)$ is supposed to determine a natural transformation $H_A \to F$, then its value on a morphism $f: A \to X$ is forced: since $F$ is covariant, $F(f): F(A) \to F(X)$ carries $u$ to an element of $F(X)$. Thus for every object $X$ we define
\begin{align*}
(\alpha_u)_X: \operatorname{Hom}_{\mathcal C}(A,X) &\to F(X) \\
f &\mapsto F(f)(u).
\end{align*}
Now we check naturality. Let $g: X \to Y$ be a morphism in $\mathcal C$. Naturality requires the equality of functions
\begin{align*}
F(g) \circ (\alpha_u)_X = (\alpha_u)_Y \circ H_A(g)
\end{align*}
from $\operatorname{Hom}_{\mathcal C}(A,X)$ to $F(Y)$. To prove equality of functions, evaluate both sides at an arbitrary morphism $f: A \to X$. The hom-functor acts by postcomposition, so $H_A(g)(f)=g \circ f$. Therefore
\begin{align*}
F(g)\bigl((\alpha_u)_X(f)\bigr)
&= F(g)\bigl(F(f)(u)\bigr) \\
&= (F(g) \circ F(f))(u) \\
&= F(g \circ f)(u) \\
&= (\alpha_u)_Y(g \circ f) \\
&= (\alpha_u)_Y\bigl(H_A(g)(f)\bigr).
\end{align*}
The equality $F(g) \circ F(f)=F(g \circ f)$ is exactly covariant functoriality. Hence $\alpha_u$ is a natural transformation, and this construction defines a function
\begin{align*}
\Psi: F(A) &\to \operatorname{Nat}(H_A,F) \\
u &\mapsto \alpha_u.
\end{align*}
[/guided]
[/step]
[step:Show evaluation after construction recovers the original element]
Let $u \in F(A)$. By definition of $\Theta$ and $\Psi$,
\begin{align*}
(\Theta \circ \Psi)(u)
&= \Theta(\alpha_u) \\
&= (\alpha_u)_A(\operatorname{id}_A) \\
&= F(\operatorname{id}_A)(u) \\
&= \operatorname{id}_{F(A)}(u) \\
&= u.
\end{align*}
The fourth equality uses functoriality of $F$ on identity morphisms. Thus $\Theta \circ \Psi = \operatorname{id}_{F(A)}$.
[/step]
[step:Show construction after evaluation recovers the original natural transformation]
Let $\alpha \in \operatorname{Nat}(H_A,F)$, and define $u := \Theta(\alpha)=\alpha_A(\operatorname{id}_A) \in F(A)$. We prove that $\Psi(u)=\alpha$.
Let $X \in \operatorname{Ob}(\mathcal C)$ and let $f \in \operatorname{Hom}_{\mathcal C}(A,X)$. Naturality of $\alpha$ for the morphism $f: A \to X$ gives
\begin{align*}
F(f) \circ \alpha_A = \alpha_X \circ H_A(f).
\end{align*}
Evaluating both sides at $\operatorname{id}_A \in \operatorname{Hom}_{\mathcal C}(A,A)$ yields
\begin{align*}
F(f)\bigl(\alpha_A(\operatorname{id}_A)\bigr)
&= \alpha_X\bigl(H_A(f)(\operatorname{id}_A)\bigr) \\
&= \alpha_X(f \circ \operatorname{id}_A) \\
&= \alpha_X(f).
\end{align*}
Since $u=\alpha_A(\operatorname{id}_A)$, the left-hand side is
\begin{align*}
F(f)(u)=(\alpha_u)_X(f).
\end{align*}
Therefore $(\alpha_u)_X(f)=\alpha_X(f)$ for every object $X$ and every morphism $f: A \to X$. Hence $\alpha_u=\alpha$, so $\Psi \circ \Theta=\operatorname{id}_{\operatorname{Nat}(H_A,F)}$.
[guided]
Let $\alpha: H_A \to F$ be an arbitrary natural transformation. The evaluation map extracts the element
\begin{align*}
u := \Theta(\alpha)=\alpha_A(\operatorname{id}_A) \in F(A).
\end{align*}
We must show that rebuilding a natural transformation from this $u$ gives back the original $\alpha$.
Fix an object $X \in \operatorname{Ob}(\mathcal C)$ and a morphism $f: A \to X$. Naturality of $\alpha$ applied to the morphism $f: A \to X$ says that the following two functions from $\operatorname{Hom}_{\mathcal C}(A,A)$ to $F(X)$ are equal:
\begin{align*}
F(f) \circ \alpha_A = \alpha_X \circ H_A(f).
\end{align*}
Now evaluate this equality at the identity morphism $\operatorname{id}_A$. Since $H_A(f)$ acts by postcomposition, we have $H_A(f)(\operatorname{id}_A)=f \circ \operatorname{id}_A=f$. Therefore
\begin{align*}
F(f)\bigl(\alpha_A(\operatorname{id}_A)\bigr)
&= \alpha_X\bigl(H_A(f)(\operatorname{id}_A)\bigr) \\
&= \alpha_X(f \circ \operatorname{id}_A) \\
&= \alpha_X(f).
\end{align*}
Because $u=\alpha_A(\operatorname{id}_A)$, this says
\begin{align*}
(\alpha_u)_X(f)=F(f)(u)=\alpha_X(f).
\end{align*}
The object $X$ and morphism $f: A \to X$ were arbitrary, so every component function of $\alpha_u$ agrees with the corresponding component function of $\alpha$. Hence $\alpha_u=\alpha$, which is precisely $\Psi(\Theta(\alpha))=\alpha$.
[/guided]
[/step]
[step:Conclude that evaluation is a bijection]
The maps
\begin{align*}
\Theta: \operatorname{Nat}(H_A,F) &\to F(A), &
\Psi: F(A) &\to \operatorname{Nat}(H_A,F)
\end{align*}
satisfy
\begin{align*}
\Theta \circ \Psi &= \operatorname{id}_{F(A)}, &
\Psi \circ \Theta &= \operatorname{id}_{\operatorname{Nat}(H_A,F)}.
\end{align*}
Therefore $\Theta$ is bijective, with inverse $\Psi$. This proves that natural transformations $\operatorname{Hom}_{\mathcal C}(A,-) \to F$ are in bijection with elements of $F(A)$.
[/step]