Ok, this is what I think:
Tachyon's encrypted disk contains the truth about Bree's past, that Bree needs to learn at the right time. Her parents may be descendants of Aliester Crowley, the guy who is on Bree's bedroom wall.
Also, her parents could also be the people that Gemma was talking about, the thing about the girl completeing the ceremony but then dissapearing. Bree says in 'I Completed the Ceremony' that after the ceremony, she needs to be completely disciplined after the ceremony finishes.
But after the previous girl completed the ceremony, she dissapeared, and The Order lost her, therefor they moved onto the next person or descendant, Bree.
But Daniel found out everything about the whole ceremonial type thing over the internet and managed to talk Bree out of it because she didn't know enough. Noone did.
So Bree went to Daniels, which The Order didn't like and tried to use Bree's parents to get to her by kidnapping them. But they left the message in P. Monkey.
Bree then went on he road and started taking advice from Gemma, who seemed to have control on things, but then turned out to be working for The Order, but in her videos, she contradicted herself alot, telling Bree to do some things that would help her, but then telling her to do stuff such as go home.
I believe The Order were using Gemma, but she let her concious get the better of her so tried helping Bree when she could.
The Gemma dissapeared after telling Bree she was being watched because The Order must have realised she was also hleping Bree so stopped making her post videos.
That's where Tachyon and Brother come in. In the video where Daniel filmed the fake ceremony, you can see Brothers SUV while they are driving up the mountain. Brother has been keeping tabs on them for ages now and watching their every move.
He finds the truth about Gemma and plans to kill her, but doesn't, which is why he apologises to Tachyon in his latest Voicemail message. Gemma goes into hiding.
Bree and Daniel find Jonas. They live with them while Daniel finds out about the Injections and cameras in his and Bree's bedrooms. He scarpers and lives with Jonas too after realising he is REALLY in this stuff...
Then of course Bree's dead gets in touch with Bree and they get together. I believe Bree's dad started telling Bree EVERYTHING he knew, but not being very high, he didn'#t know much. The Order jump him and I really believe that they DO kill him. They don't touch Bree because they werne't her real parents, so have no link to Aliester Crowley, unlike Bree. Therefor they dont touch her, which Jonas picks up on.
Then Daniel gets kidnapped and they get him to do the video. obviuosly the whole Bree/Tachyon link get's setup and they get ready to rescure Daniel, which they do.
Tachyon gives the disk to Bree, she even says that Tachyon learnt everything about The Order and is just investigating OpAphid. Tachyon knows Bree is a descendant which is why the Order NEEDS Bree and only Bree for the ceremony.
OpAphid are a part of The Order that will benefit hugely from the Ceremony. I'm not sure why, but I feel that they will get alot out of the ceremony, which is why they do anything to rid of Tachyon and Brother, and get Bree.
It also explains why no-one EVER touches Bree, because they can't have anyone else.
I hope you guys understand this, and that it's not TOO long... First post too

Replies would be cool.
I probably have loadsa loopholes and look forward to getting completely ripped apart

Rik
EDIT: Forgot to mention that Bree says she won't talk to her mother for a while. Maybe this is becasuse her mother is high in The Order and helped out with things that Bree didn't agree with, so Bree doesn't want to talk to her. I'm not too sure about this...