- When the dragons sleeping beneath the earth threaten to awaken and wreak havoc around the world, Flynn returns to help find their hidden treasure.
- When the weather is going wild, the team tries to find out what's going on. That's when Flynn returns and tells them what's going on is the dragons are at war. That's when someone who represents one faction comes and tells them that one of their treasures has been stolen. And when they learn where it is, they need to steal it back and they would need Jones but because he was the one who first spoke to the representative, he needs to stay and entertain him and listen to his grievances and wait for the other representatives to arrive and mediate. So Flynn and the others go and when they get it, whoever touches it, his or her personality changes.—rcs0411@yahoo.com
- Flynn returns to the Annex to help the team with the latest magical threat: dragons. The dragons live beneath the earth and when angered, they awaken. Dragons can cause all kinds of trouble, including strange weather and natural disasters such as earthquakes. Eastern dragons (the Fei Lung) and Western dragons have had a blood feud stretching back many millennia and a fight between them could lead to widespread destruction. Eve has mixed feelings about Flynn's return, as she feels he is disrupting the team and undermining her authority as team leader.
The team meets a representative from the Eastern dragons, a lawyer named Mr. Drake, who informs them that the Western Dragons have stolen the Mystic Pearl of the Fei Lung. He demands that it be returned or else the dragons will go to war. Due to a misunderstanding, it is up to Ezekiel to deal with Mr. Drake, who has brought with him a long list of grievances the Eastern dragons wish to see addressed in an Intercession. Jenkins takes on the task of assisting Ezekiel with the details of the Intercession, but the two are often at odds - Jenkins feels that Ezekiel is not taking things seriously and cannot be trusted with a task of this importance.
Meanwhile, Flynn, Eve, Jacob, and Cassandra head to Vatican City in search of the lair of the Western Dragons, which lies underneath the city. After a quick escape from the Vatican, the team makes their way through puzzles and traps to retrieve the Mystic Pearl. However, the Pearl secretly holds the Apple of Discord, which brings out the worst possible version of whomever holds it. The Apple first infects Jake, who tries to rearrange a local art gallery by force. Flynn, Eve, and Cassandra encounter one of the Western Dragons, who tells them that they were not the ones behind the theft of the Pearl. The team manages to disarm Jacob, but the Apple is transferred to Cassandra. Using math, she is able to easily take down Lamia, and then sets her sights on causing a massive power grid failure. While the team manages to disarm her, Eve and Flynn end up with the Apple -- first sharing it, then fighting over it when it becomes clear that their evil visions for the future are incompatible. Lamia nearly gets killed when she interferes in the fight, and in the end, Flynn escapes with the Apple.
Back in the Annex, Ezekiel finds himself having to chair a Conclave of several magical factions (including the Jinn, the Fae Legions, and the Iron Kingdom) in which they must try to resolve their disputes peacefully. Unfortunately for them, things take a turn for the worse when Dulaque shows up, trying to remove the Library from its historical role as arbiter among them. Ezekiel is upset when Dulaque's appearance causes Jenkins to leave, but Jenkins eventually comes back to help try to keep things under control. Dulaque's play for power is in full swing when the session is interrupted by a power-crazed, Apple-holding Flynn. Happily, the team is able to get Ezekiel close enough to pickpocket the Apple away and Flynn convinces the conclave attendees (except Dulaque) of the necessity of the Library.
The team is deeply concerned about what will happen to Ezekiel when he holds the Apple, but it turns out that he is immune -- he is already the worst version of himself. Ezekiel also realizes that Mr. Drake was the one to originally steal the Pearl, and prevents him from causing any more trouble.
Finally, Jenkins has a private moment with Dulaque and tells him off, knowing that he was the one to wake the dragons and cause all of the trouble that the team just had to face, all for his own agenda. Dulaque tries to offer Jenkins the opportunity to join his side, but Jenkins says that what they once had is gone now.
Flynn is impressed with the work Eve has done, so he offers her transfer papers to go from NATO to Guardian permanently and says he'll stay if she does. Eve signs the papers, but reminds him that he must go back out and recover the main Library.
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