Well, the first thing that jumps out at me is that your first plot, although having the right shape has a maximum of 0.1. It should be 1.0. Next, the time scale in the second plot starts at -6 seconds. What you've got there is a time machine.
BUT, I think your main problem is that you've got a bad transfer function. 1/(s^2 +6s +9)==> 1/(s+3)(s+3). Your step response is then: 1/(s(s+3)(s+3)), which is of the form: 1/s(s+a)(s+b). If you look at any table of Laplace transforms you'll see that the inverse transform of your step response is: 1/(a+b) * {1-[(be^-at)-(ae^-bt)]/(b-a)}. You've got a denominator of zero, which makes everybody unhappy.