Alias Question. . .

I've only seen parts of Season 1 & 2 of Alias. I honestly, have no clue what season they are in now. The last episode I saw, I think, ended with Sidney finding out that her mother was behind some evil group. My memory is pretty foggy but I do remember that her mom seemed to be the enemy. I may have seen some episodes after that but the impression I got was the relationship of mother & daughter was not good.

Fast forward to this season's premiere. As I said before, most of my knowledge (which is very sparse) is with seasons 1 & 2. I'm watching the premiere and I'm digging it because this show knows how to bring the good. There was one plot point that bothered me. Sidney was harbouring angry feeling towards her father because he ordered the death of her mother (his wife). He had been estranged from his wife. Sidney never grew up with her mom. The mom that she did know was a very bad lady. Here is my question, what am I missing? Why does/did Sidney hate her father for ordering the death of her mother? From what I know, she didn't like her mother. Her mother was obviously out to get Sidney. Why the hate? I'm thinking I must have missed a major plot point which is easy since I have seen very few episodes.

The people I were with didn't understand either. The only thing I coud guess was that it was still her mother. She wasn't good but she was the one to bring her into the world. Despite everything, she still loved her because she was mom. Was there more than this? Did Sydney at some point connect with her mother? I had the impression they were always at odds.

I appreciate the enlightenment. I understand this is total geekdom. I have writer's block today and decided to resort to this. I think I have an excuses to start grabbing old seasons of Alias on DVD. I need to catch up.