After Logan's escape, the Weapon X Program attempted to get back on track. Almost immediately, however, they suffered another escape when the back-up subject, codenamed Feral, broke free from her experimental tank and disappeared into the wilderness after Logan. Feral apparently escaped before the Adamantium bonding process could be applied to her, and even before her memory engrams could be uploaded into the Shiva program.
The Professor pulled back from further Adamantium experiments at this point. The Weapon X Program began focusing on establishing their sleeper agents using the same memory manipulation techniques pioneered with Logan. Despite his escape, the mental conditioning and false memory architecture in Logan's mind had been soundly tested, and the Weapon X Program believed it could be easily duplicated in other, susceptible agents.
Weapon X somehow gained access to the Team X files (likely through their CIA sponsors) and brought in all of Logan's former teammates from Team X as test subjects, including Sabretooth, Fox, John Wraith (Kestrel), Mastodon and David North (Wildcat). Cell samples from Wolverine (and possibly Sabretooth) were cultivated to produce a low-level derivative of their healing factor. Injected into the Team X subjects who needed it, this "age suppression factor" enabled Fox, North, Wraith and Mastodon to remain young and vital decades past their prime.
Despite this moderate success, the Professor's time in the sun was clearly done. The Weapon Plus Program quickly moved beyond Weapon X, using more advanced theories and technologies for their latest weapons such as genetic manipulation, nanotech and time dilation. John Sublime was promoted over Thorton to the head of Weapon Plus, and he officially pulled all funding from Weapon X around the time Weapon XIII was in production. Undeterred, the Professor attempted to keep Weapon X running without Sublime's support, using his own government connections.
This apparently didn't last, however, as Weapon X eventually closed its doors as an active project. The Professor and Hines, at least, remained employed by the government as the program was absorbed into the Department of Agriculture as the "Pest Control Section." The Weapon X test subjects were mindwiped and released back into society. The remnants of Weapon X were left with only a meager budget and resources, sufficient only to monitor the inactive agents and protect Weapon X's secrets if they were somehow threatened. The Professor's dreams of power and success were quashed permanently, leaving him with nothing more than a small office in Washington D.C., a permanent position monitoring his failures for the government, and his own bitter memories.