During the Second Tiberium War and its aftermath, she was the director of the Daedalus Team, a team of scientists dedicated to Tiberium research and translating the alien and unreadable Tacitus. The doctor had a cordial, even friendly, relationship with Forgotten leader Tratos, in large part due to their joint efforts to decipher the mysteries of the Tacitus and Tiberium.
At Tratos' request, Dr. Boudreau oversaw an expeditionary force to Cairo to recover the Tacitus, Kane's other research and deliver it safely to Tratos. This was not without risk, as although GDI forces held the remnants of Kane's Cairo facility, Nod snipers harassed the team, despite the strong winds buffeting the site. Whilst Dr. Boudreau oversaw the loading of the Tacitus and all of Kane's research onto the Kodiak, she was not aboard it when it crashed during an Ion Storm in Egypt, but she watched it go down from her position at the Cairo facility.
Later, she berated General Paul Cortez, commander of GDI's Southern Cross base, and her ex-husband to boot, for allowing Tratos to be assassinated by Nod forces, setting their research back months, if not years. Furthermore, she had to deliver the news that within a year, the Earth's atmosphere would become 100 percent toxic to humans, thanks to the rate of Tiberium poisoning of organic life on Earth. In a somewhat controversial move, she suggested using CABAL to translate the Tacitus, as the Nod AI had helped Tratos translate parts of it during the 2nd Tiberium War. A GDI commander was despatched to capture CABAL's data core for this purpose.
With CABAL captured, and reconstructed in the Daedalus facility, the Tacitus translation began, though not before a second piece of the Tacitus was recovered from South America. With the Tacitus complete, CABAL's captured Cyborgs turned on the GDI forces at the facility, forcing Dr. Boudreau to flee for her life.
Following her rescue, Dr. Boudreau gave a brief lecture on the tactics CABAL employed to gain more 'recruits' for his army, and informed the GDI Commander that her team had successfully implanted a virus in one of the cyborgs (Huey), with the intention of getting him into CABAL's production facility to disrupt the expansion of CABAL's army, and give the GDI-Nod alliance a chance to destroy CABAL's core.
After the operation, the Daedalus team recovered the Tacitus, now fully intact, the data proved to be perfectly readable, although absolutely massive in its information content. Before cutting communications with Southern Cross to concentrate on the information, she joked that although Cortez and her had made a good team during the crisis, the same could not be said for their marriage.
It is presumed that after the crisis, Dr. Boudreau continued to work on processing the Tacitus data. Amongst the deciphered content was that sonic disrupters could be used to break down Tiberium, and that there would be a foreshadowed Scrin invasion by the events of the Third Tiberium War. Boudreau's work, coupled with that of Dr. Mobius and his daughter, were vital to the survival of the human race after the Firestorm incident, as their discoveries led to the decontamination of regions and ensuring the safety and sustainability of GDI's Blue Zones.