First, let's define $b(n) := 3^n-a(n)$, the number of ternary strings that don't contain the substring $11$, as it is easier to find a recurrence relation for this in the fist place.
Since the empty string and any of the strings of length $1$ do not contain the substring $11$, we find that $b(0)=1$ and $b(1)=3$.
Now, for $n\ge 1$, we try to build a feasible string (not containing $11$) of length $n+1$. Such a string can start with either $0$ or $2$ followed by any feasible string of length $n$, or it can start with $1$ followed by either $0$ or $2$ and then any feasible string of length $n-1$. This leads to the recurence formula $b(n+1)=2\cdot b(n)+2\cdot b(n-1)$.
Now, since $b(n)=3^n-a(n)$ for all $n \ge 0$, we see that
$$\begin{align}
3^{n+1}-a(n+1)&=2\cdot(3^n-a(n))+2\cdot(3^{n-1}-a(n-1))\\
\iff a(n+1)-2\cdot a(n)-2\cdot a(n-1)&=3^{n+1}-2\cdot3^n-2\cdot3^{n-1}\\
&=3^{n-1}
\end{align}$$
This is a recurrence relation for $n \ge 1$, but it contains the term $3^{n-1}$ which we still can eliminate for $n \ge 2$ in the following way:
$$\begin{align}
3^{n-1}&=3\cdot 3^{n-2}\\
\iff a(n+1)-2a(n)-2a(n-1)&=3\cdot(a(n)-2a(n-1)-2a(n-2))
\end{align}$$
Solving this for $a(n+1)$, we find the linear recurrence relation for all $n \ge 2$:
$$
a(n+1)=5\cdot a(n)-4\cdot a(n-1)-6\cdot a(n-2)
$$
Of course, we have to specify the initial values for the recursion, which are $a(0)=a(1)=0$ and $a(2)=1$.
Added:
Just in case you need an explicit formula:
$$
a(n) = 3^n+\frac{2-\sqrt{3}}{2\sqrt{3}}\left(1-\sqrt{3}\right)^n-\frac{2+\sqrt{3}}{2\sqrt{3}}\left(1+\sqrt{3}\right)^n
$$