I had a hunch and followed it.
A huge Bug in mission control template.
You have to install all the other extensions that get installed with the template first before uninstalling the template from the extension manager.
Like I said I renamed the missioncontrol folder in plugins/system/ and I got my site working back.
Then I checked the extension manager and saw a "site" plugin called Missioncontroller. By Rocket theme. I tried uninstalling it, and it did not work(obviously since I had renamed that file

)
I then reinstalled the rt_missioncontrol template.
Then I uninstalled all the plugins including missioncontroller and then at the end uninstalled the admin template and everything working fine.
I had checked my database through phpmyading and there were two tables of Rt. .Once was Audit and the other I forgot.
These two tables were left behind.
So the flaw is in the template while it successfully installs all these additional plugins it does not uninstall them well and that crashes your entire website.
Its a very grave error and I am still surprised to see that RT team and not done anything about or identified the problem yet.
So Greg Gillham if you are worried about any "residual effect" Please follow the above.
There is a "residual" junk entries in the database. So this takes care of it.