Alter of the Nine (spoilers possible)

[Gigantor]

When i goto fix what i have done wrong in the Temple of the Nine, all i get is negitive messages, and when i try and use the alter of the nine i get a message saying Repent you crimes, wicked one. Have i totally screwed my game or do i still have a chance of continueing with the story line?

[Relush]

Don't worry, you didn't screwed anything.
That's because you did some of the thieves/dark brotherhood quests (you can call it crimes) , and now you have a high Infamy. If you want to pray, you should do quests from the fighters/mages guild, or close oblivion gates (good deeds). This is how you will repent your crimes.

[Dragon Reborn]

just doing quests the main quest in general gets you alot of fame