Though seemingly an ally, he released tuberculosis inside Ruben in an attempt to steal bubonic plague to sell to the highest bidder, even if they were terrorists. His crimes are exposed when bubonic plague crawled out of his backpack.
His motive for his crimes are due to him holding an immense dislike for Dr. Xenon Bloom. Once he is found out, he holds Annie hostage and Morty, who had fallen for her, attacks Poncho in retaliation. Poncho laughs at Morty's attempts and pushes him aside. The bubonic plague bites Poncho's shoulder hurting him. As he attempts to get bubonic plague off of him, he falls off the railing in the large intestine and is never seen again.
Even if he had survived the fall, he was likely crushed to death in the pile of feces that erupted when the sphincter dam burst due to Ruben's death creating a corpse load.