One of the big questions, of course, is "what's with those Strausses?" So here for the first time outside of the GM's twisted head is the whole story.
Thielo and Johannes Strauss were born twins, but their parents were killed in an accident just afterwards and they were adopted by different branches of the Strauss family. Soon afterwards there was a falling-out and the two branches never talked to each other again. Thielo grew up happy and well adjusted. Johannes grew up in a bad home, poor, and angry. Eventually his adopted parents told him he was adopted, and he found out about Thielo. Here was someone just like him, only with a better life.
Johannes became a personamancer and started pretending to be other people, all the while keeping tabs on Thielo. He followed to the US, and there decided he would replace Thielo and take the good life for himself. While Alexandra was away for a week, he meets with Thielo and tells him about how they are twin brothers. They swap life stories and generally bond. Then Johannes kills Thielo and hides his body. When Alexandra comes back, he pretends to be Thielo.
However, he doesn't love Alexandra, and starts fooling around. She notices after a while and confronts him about it, he denies it, she starts getting very angry. He realizes what is going to happen and makes a mask of Thielo which he puts on a homeless man. That man goes home and programmed by the mask really makes Alexandra angry. She shoots him with a crossbow and buries him in the yard (the body found in their yard during the game). Later, feeling bad about the whole thing, she makes a clockwork replacement and forgets the entire incident.
Another question is "what's with Gavin?" This one is pretty simple. Gavin L'Or was the godwalker of betrayal. He ascended. Out of the Clergy came the previous Betrayer, passing through the house of renunciation, into Gavin's body. Lots of people call him Gavin, so he thinks he is. He becomes the knight protector to atone for his past deeds, or Gavin's past deeds, anyway.
Gustav Hawley's plan is another enigma. Once you realize he was nuts, it all falls into place - he needed one more big memory to make his dream woman, and realized that the memory of dying would be big enough. And he could catch himself in a ghost trap to complete the work! Unfortunately, then he was in the ghost trap. This is what happens when you use up all of your memories.
The coyotes were in fact just normal coyotes that were effected by the mystic waves of the Paranoid close to ascension. They just woke up one morning and decided to be smart and mug people.
"Why did Esteban's brother get killed?"
Esteban's brother sold bad heroin (cut heavily with inert material) to Anne Covington and Mubarek. They wanted it to do a ritual reenacting the Osiris myth to give Mubarek immense control over the dead. He needed to be mostly immune to pain during the ritual, however, which involved symbolically cutting him into pieces as happened to Osiris. With the bad heroin, he wasn't.
Once he recovered, Anne and Mubarek tracked down Jesus and got their revenge by killing him and stealing his soul as well, using it as an undead servant. The moral of the story is don't sell death mages bad heroin. Or maybe that drugs are bad for you.
Eating human meat can make you immortal if it's properly prepared, but unless you're a pretty exceptional person you eventualy shrivel into a little naked swamp monkey. Then you're still immortal, but you're a crazy little naked thing that lives in the swamp, so it's less fun. The fancy restaurant was feeding human meat to people because the owner, who had joined the whole eating-people group, went a little mad and decided that he would corrupt the world to join him in his terrible obsession, and then it wouldn't be evil and he wouldn't be a bad person. Or something like that. When you're eating people once a week, your mind is liable to come up with some weird ideas.
"Why did the next universe turn out like that?"
A lot of the last ascensions were pretty American archetypes. It's been the American century recently. And the team's refusal to assassinate the president, instead getting Alex Abel to be president in a moment of healing for the country (forced or not) greatly increased the stock of America in the giant universe reorganization. So history is reset to the beginning of the country, to give it another go and see how it turns out this time. Various archetypes did indeed speak for the team and so they come through.
Gavin, however, used his channel at the end of the last universe to take anything bad that would happen to Angelina on himself. He succeeded well enough to cover the entire team. But of course, with his knowledge he cannot be allowed to live. So he dies.
Thielo (the mechanical man) somewhat makes it into the next universe as Thielo the computator. In the remade universe, it is easier to make thinking machines - this is because of the ascension of a computer simulation of a human into one of the 333 seats. Perhaps the revolution will be easier with Alexandra's machines assisting. Gwen, who always pretty much wanted to be a real girl, is in the new universe. Sometimes the innocent are in fact rewarded.