Leaving off from the previous issues, Silver's team (consisting of Larry Lynx and Shard) is in hot pursuit of Geoffrey St. John. After losing him, they report back to Harvey Who, who sends them off to meet up with the rest of the team (Elias, Leeta and Lyco) and ensure they are ok. After reuniting, the team discusses their findings and speculations as to what Ixis Naugus is up to. However, unbeknownst to them, Geoffrey is lurking in the shadows and watching their every move and he soon realizes who is after him and his master.

Meanwhile, back to Silver and the team, they are still trying to understand what Naugus' true intentions are. This is when Silver suggests that perhaps they should ask Geoffrey. Elias finds the idea mad, but Silver believes Geoffrey is just caught up in this whole mess. So they decide to give Silver's plan a shot and sure enough, they get their answers without hassle. They learn that Naugus plans to take control of the council.

With Naugus' motives discovered, the Secret Freedom Fighters must now prevent the council from having their meeting. Larry Lynx attempts to use his bad luck to foil the council's attempts into the meeting hall, while Silver, Elias, Shard, Leeta, and Lyco go after Naugus in the magic chambers under the city.

Naugus (and Geoffrey's) plan is foiled and the magic crystal and entire chamber are destroyed, rending their plan useless. The Secret Freedom arc ends with Harvey Who attempting to aid Silver in his goal of finding the traitor. We don't see who it is, but all will be revealed in the normal comics in due time.