We are given the quadratic equation:
\[
x^2 + 3(a + 3)x - 9a = 0.
\]
Step 1: Condition for Double Roots
For the given equation to have double roots, its discriminant must be zero:
\[
\Delta = b^2 - 4ac = 0.
\]
Here,
\[
a = 1, \quad b = 3(a + 3), \quad c = -9a.
\]
Calculating the discriminant:
\[
[3(a + 3)]^2 - 4(1)(-9a) = 0.
\]
\[
9(a + 3)^2 + 36a = 0.
\]
Expanding:
\[
9(a^2 + 6a + 9) + 36a = 0.
\]
\[
9a^2 + 54a + 81 + 36a = 0.
\]
\[
9a^2 + 90a + 81 = 0.
\]
Step 2: Solve for \( a \)
Dividing by 9:
\[
a^2 + 10a + 9 = 0.
\]
Factoring:
\[
(a + 9)(a + 1) = 0.
\]
Thus,
\[
a = -9, \quad a = -1.
\]
Step 3: Finding \( \alpha \) and \( \beta \)
Since \( \alpha>\beta \), we take:
\[
\alpha = \text{larger root}, \quad \beta = \text{smaller root}.
\]
For each \( a \):
- \( a = -9 \), the equation becomes:
\[
x^2 + 3(-9 + 3)x + 9(9) = 0.
\]
\[
x^2 - 18x + 81 = 0.
\]
Roots:
\[
\alpha = 9, \quad \beta = 9.
\]
- \( a = -1 \), the equation becomes:
\[
x^2 + 3(-1 + 3)x - 9(-1) = 0.
\]
\[
x^2 + 6x + 9 = 0.
\]
Roots:
\[
\alpha = -3, \quad \beta = -3.
\]
Step 4: Minimum Value of \( x^2 + \alpha x - \beta = 0 \)
Substituting \( \alpha = 9 \), \( \beta = 9 \):
\[
x^2 + 9x - 9 = 0.
\]
Minimum value of the quadratic equation is found at:
\[
x = -\frac{9}{2}.
\]
Substituting:
\[
\left( -\frac{9}{2} \right)^2 + 9 \times \left( -\frac{9}{2} \right) - 9.
\]
\[
\frac{81}{4} - \frac{81}{2} - 9.
\]
\[
\frac{81}{4} - \frac{162}{4} - \frac{36}{4}.
\]
\[
\frac{81 - 162 - 36}{4} = \frac{69}{4}.
\]
Thus, the minimum value is:
\[
\boxed{\frac{69}{4}}
\]