Hint
let $s\le t$ and
$$P(s,y\,;\,t,x)=P(r_t\le x|r_s=y)$$
The transition probability $P(s,y\,;\,t,x)$ satisfy Kolmogorov bachward equation
$$\frac{\partial P}{\partial s}+\kappa (\theta -{{r}_{s}})\frac{\partial P}{\partial r}+\frac{1}{2}{{\sigma }^{2}}{{r}_{s}}\frac{{{\partial }^{2}}P}{\partial {{r}^{2}}}=0\quad \,\,(1)$$
$$P(s,y\,;\,t,x)=\delta_x\,\,,\,\,s\to t$$
we define
$$f(\tau,u,{{r}_{s}})=\mathbb{E}[e^{\large{iur_t}}|\,r(s)]$$
where $\tau=t-s$. We know CIR process is a affine process thus
$$f(\tau ,u,{{r}_{s}})=\exp [A(\tau\,,\,u)+B(\tau\,,\,u){{r}_{s}}]$$
where
\begin{align}
& A(0\,,\,u)=0 \\
& B(0\,,\,u)=iu \\
\end{align}
Substitute for $f$ in $(1)$
$$\frac{\partial f}{\partial s}+\kappa (\theta -{{r}_{s}})\frac{\partial f}{\partial r}+\frac{1}{2}{{\sigma }^{2}}{{r}_{s}}\frac{{{\partial }^{2}}f}{\partial {{r}^{2}}}=0\,.$$
Note
\begin{align}
& \frac{\partial f}{\partial s}=-\left( \frac{\partial A}{\partial r}+{{r}_{s}}\frac{\partial B}{\partial r} \right)f \\
& \frac{\partial f}{\partial r}=B\,f \\
& \frac{{{\partial }^{2}}f}{\partial {{r}^{2}}}={{B}^{2}}f \\
\end{align}
as a result
$$\frac{1}{2}{{\sigma }^{2}}{{r}_{s}}{{B}^{2}}+\kappa (\theta -{{r}_{s}})B-\frac{\partial B}{\partial s}{{r}_{s}}-\frac{\partial A}{\partial s}=0$$
set $r_s=0$, then
$$\frac{\partial A}{\partial s}=\kappa \theta B$$
setting $r_s=1$,then
$$\frac{\partial B}{\partial s}+\kappa B=\frac{1}{2}{{\sigma }^{2}}{{B}^{2}}$$
The first equation is an ordinary differential equation the second is Riccati equation. If You solve these equations then
$$f(t-s,u,{{r}_{s}})={{\left( 1-\frac{iu}{{{c}_{t}}} \right)}^{-\frac{2\kappa \theta }{{{\beta }^{2}}}}}\exp \left( \frac{i\,u{{e}^{-\kappa (t-s)}}}{1-\frac{iu}{c_t}}{{r}_{s}} \right)$$
where
\begin{align}
& {{c}_{t}}=\frac{2\kappa }{{{\beta }^{2}}\,[1-{{e}^{-\kappa (t-s)}}]} \\
& k=\frac{4\kappa \theta }{{{\beta }^{2}}} \\
& {{\lambda }_{\,t}}=2{{c}_{t}}\,{{r}_{s}}{{e}^{-\kappa (t-s)}} \\
\end{align}
By application Inverse Fourier Transform we have
$$p(s,y;\,t,x)=\frac{1}{2}{{e}^{-\frac{1}{2}(2{{c}_{t}}{{r}_{t}}+{{\lambda }_{t}})}}{{\left( \frac{2{{c}_{t}}{{r}_{t}}}{{{\lambda }_{t}}} \right)}^{\frac{k}{4}-\frac{1}{2}}}{{I}_{\frac{k}{2}-1}}(\sqrt{2{{c}_{t}}{{r}_{t}}{{\lambda }_{t}}})$$