1. Xenocrates had been teased about his size by the Supreme Blade, and he now thought that he was like 'the overweight kid that was always picked last in the sports team'. In Midmerica, he would've been thought as impressive, but now he looked silly compared to the other scythes in the World Council.
2. By misplaced, Faraday could simply be implying about the hidden books while keeping them a secret.
3. Goddard wouldn't let her have what she wanted, so she decided that he shouldn't have what he wanted as well. This is why she lets Rowan escape.
4. They manage to find the Marshall Atolls, and they discover that the center Atoll, Kwajalein is the Land of Nod.
5. The Thunderhead can't operate on Endura because of scythe-stat separation. So, humans have to fix the glitches manually, just like in the mortal age. Either that or it's the doing of Goddard, who hacked into the system, which caused the sinking of Endura.
6. The World Council saw themselves in Anastasia, and since they were power hungry before, they assumed that Anastasia was also power hungry.
7. She tricked the two into going into the cube and locking them in. Since water temperature is always a few degrees above freezing, the air-tight chambers would preserve the two until they were found and revived.
8. This is probably in a plan of the Thunderhead's. In previous plans, the Thunderhead would have to have a connection with Greyson in private. For example, Greyson and Agent Traxler would communicate in secret while Greyson was an unsavory. This time, the Thunderhead marked everyone unsavory except for Greyson, so that meant nobody can communicate with the Thunderhead except Greyson, and so this could be how Greyson can communicate with the Thunderhead secretly. This factor must be part of the Thunderhead's plan, otherwise it wouldn't try to communicate with Greyson more than once.