I assume that you're satisfied with the code you have for the nine plots, and hence that the remaining task is to group the nine plots on a page. I suggest you create a dedicated environment called, say, "smallpic" to house each file and associated text. That way, you can save yourself a lot of repetitive typing.
\documentclass[12pt]{article}
\usepackage[demo]{graphicx} % remove 'demo' option in real document
\usepackage{caption}
\newenvironment{smallpic}{\begin{minipage}{0.3\textwidth}\small}
{\end{minipage}}
\usepackage{pgfplots}
\begin{document}
\begin{figure}
\caption{Nine graphs} \label{fig:ninegraphs}
\begin{smallpic} % Fig. 1
\begin{tikzpicture}
\begin{axis}[
width = 5.6cm,
height = 5cm,
axis y line = middle,
axis x line = middle,
grid style = {dashed, gray!50},
grid = both, % Switch on the grid lines
%ymajorgrids = true,
%xmajorgrids = true,
minor ytick = {-7,-6,...,3},
minor xtick = {-5,-4,...,5},
xmin = -5,
xmax = 5,
ymin = -7,
ymax = 3,
%xlabel = $x$,
%ylabel = $y$,
]
\node at (axis cs:-2.45,-5) [blue]{$\bullet$};
\node at (axis cs:2.45,-5) [blue]{$\bullet$};
\addplot[smooth, blue, thick, domain = -2.45:2.45] {-x^2 + 1};
\end{axis}
\end{tikzpicture}
D: $-2.4 \leq x \leq 2.4$
R: $-5 \leq y \leq 1$
This is a parabola.
\end{smallpic}
\hspace{\fill}
\begin{smallpic}
\includegraphics[width=\linewidth]{fig2}
D:
R:
Function ?
\end{smallpic}
\hspace{\fill}
\begin{smallpic}
\includegraphics[width=\linewidth]{fig3}
D:
R:
Function ?
\end{smallpic}
\bigskip\bigskip
\begin{smallpic}
\includegraphics[width=\linewidth]{fig4}
D:
R:
Function ?
\end{smallpic}
\hspace{\fill}
\begin{smallpic}
\includegraphics[width=\linewidth]{fig5}
D:
R:
Function ?
\end{smallpic}
\hspace{\fill}
\begin{smallpic}
\includegraphics[width=\linewidth]{fig6}
D:
R:
Function ?
\end{smallpic}
\bigskip\bigskip
\begin{smallpic}
\includegraphics[width=\linewidth]{fig7}
D:
R:
Function ?
\end{smallpic}
\hspace{\fill}
\begin{smallpic}
\includegraphics[width=\linewidth]{fig8}
D:
R:
Function ?
\end{smallpic}
\hspace{\fill}
\begin{smallpic}
\includegraphics[width=\linewidth]{fig9}
D:
R:
Function ?
\end{smallpic}
\end{figure}
\end{document}