Attacking the compound, Nomi retreated to safety to protect her daughter Vima. However, Thon allowed himself to be attacked by the invaders, reaching out with the Force, telling Nomi she had to make a choice. It was a turning point for Nomi; she finally acknowledged her role as a Jedi. Unknowingly using a Jedi technique called Battle Meditation, Nomi was able to turn the henchmen against themselves, and during the ensuing battle, Thon and Nomi were able to repel that attackers once more. With the dangers finally behind them, and Nomi eager to learn the ways of the Jedi, Thon once again took up the role as teacher as he helped shape Nomi into a Jedi Knight.

Thon eventually took Nomi Sunrider to the Jedi planet of Ossus in order that she build her own lightsaber as well as study from the Great Jedi Library Thon did not have the luxury of on Ambria. Nomi was eventually part of a Jedi task force sent to Onderon to confront a Freedon Nadd Uprising that was occurring there. Over the next few months, Thon remained on Ossus as Onderon was liberated from the Dark Side rule of Queen Amanoa and King Ommin, and a group calling themselves the Krath launched a political coup in the Empress Teta System, and the subsequent declaration of war by the Krath on the Jedi. This action prompted a great Jedi convocation on the planet of Deneba and Thon was part of the delegation of Jedi that traveled there to discuss these turn of events.

However, the convocation was cut short by a surprise attack by the Krath, who launched an army of battle droids from space to strike against the Jedi. After the attack, Thon and the Jedi returned to Ossus to discuss plans of what to do in dealing with the Krath. On Ossus, Thon served on a makeshift council that discussed aspects of the Jedi's war with the Krath. On the council, Thon gave his input when Nomi Sunrider and Cay Qel-Droma came to the council proposing a mission to rescue Ulic Qel-Droma from his attempt to infiltrate the Krath, for they feared he was walking a fine line and was in danger of becoming seduced by the Dark Side.

Thon and the council granted permission to Cay and Nomi to carry out their plan, but Thon warned that Ulic had to return with them by his own free will; if he chose to stay, then he would have to accept the consequences of his actions. During the turn of events that threw the galaxy further and further into conflict: Ulic's declaration of his alliance with the Krath, and Exar Kun's self-proclamation of the new Dark Lord of the Sith, Thon remained on Ossus, but eventually returned to Ambria for some solitude and meditation.