In 634, Emperor Taizong, sending the senior general Li Jing to command the campaign against Tuyuhun's Busabo Khan Murong Fuyun, made Hou and Li Daozong the Prince of Rencheng Li Jing's assistants on the campaign. By spring 635, Tang forces achieved initial victories, but Tuyuhun forces then burned the grazing grass to cut the food supplies to Tang horses. Most Tang generals wanted to withdraw, but Hou advocated continued advance, and Li Jing agreed, eventually allowing complete victory, as Murong Fuyun was killed by his subordinates, allowing his son Murong Shun, whom Tang supported, to become khan . Around the new year 636, after Murong Shun was assassinated by his subordinates, Emperor Taizong sent Hou with an army to try to secure the throne for Murong Shun's son Murong Nuohebo.
Hou Junji was resentful that, despite his great achievement, he was put under arrest, albeit briefly, and in spring 643, when fellow general was sent out of the capital to serve as the commandant at Luo Prefecture , Hou tried to instigate him by asking him, "Who squeezed you out?" Zhang, in jest, responded, "Other than you, who can squeeze me out?" Hou responded, "I conquered a kingdom, but I ran into someone throwing a tamper tantrum big enough to overturn a house. What strength do I have to squeeze you out?" He then rolled up his sleeves and yelled, "I am so unhappy that I would rather die. Do you want to commit treason? I will commit treason with you!" Zhang secretly reported this exchange to Emperor Taizong, but Emperor Taizong pointed out that this was a private conversation with no corroboration, and took no action on it.
Around the same time, however, Emperor Taizong's crown prince Li Chengqian was becoming fearful because Emperor Taizong had greatly favored another son, Li Tai the Prince of Wei, and Li Tai was making designs on the crown prince position. Li Chengqian therefore gathered a group of men around him to consider overthrowing his father, including his uncle Li Yuanchang the Prince of Han, his cousin Zhao Jie , and brother-in-law Du He . Hou's son-in-law Helan Chushi , the commander of Li Chengqian's guards, was also part of the plot, and through Helan, Li Chengqian invited Hou to join the plot as well, as Hou agreed. However, he was deeply disturbed by his own involvement, and he developed insomnia. His wife sensed that something was wrong, and told him, "You, Duke, are an important official of the state, so why are you acting like this? If there is something you are doing wrong, you should report yourself so that your life can be spared." However, Hou did not do so.
Eventually, however, Li Chengqian's plot was betrayed by his guard Gegan Chengji , and after an investigation ordered by Emperor Taizong and conducted by Zhangsun Wuji, Fang Xuanling, Xiao Yu, Li Shiji, as well as responsible officials from the supreme court and the legislative and examination bureaus of government, Li Chengqian was deposed. The other conspirators, including Hou, were sentenced to death. Emperor Taizong initially considered commuting Hou's death sentence because of his accomplishments, but the other officials opposed, and Emperor Taizong stated to Hou, "I have to bid you, Duke, farewell. From now, I can only see your portrait!" Both he and Hou wept. As Hou was about to be beheaded, he stated to the general overseeing the execution, "I, Hou Junji, am not the type to commit treason, but I stumbled many times and reached this point. But as I destroyed two kingdoms as a general, please speak for me to His Imperial Majesty to request for me to have a son remaining to carry the lineage, on the basis of my accomplishments." Emperor Taizong, when he heard this, pardoned Hou's wife and children but exiled them to the modern Guangdong region, and confiscated his properties.
It was said that years earlier, after Emperor Taizong ordered Li Jing to teach Hou strategies, Hou reported to Emperor Taizong, "Li Jing is about to commit treason." When Emperor Taizong asked him why, Hou responded, "Li Jing only teaches me basic principles and does not teach me the best strategies, keeping them for himself." When Emperor Taizong asked Li Jing about this, Li Jing responded, "This is proof that Hou Junji will commit treason. China is secure right now, and the empire is united. What I taught him is sufficient to use against barbarians. If not for treasonous purposes, why would Hou want to learn all of the strategies?" At one point, Li Daozong also spoke to Emperor Taizong, stating, "Hou Junji has too much ambition and too little talent. He overvalued his achievements and found it shameful to be lower in position than Fang Xuanling and Li Jing. Even though he serves as a minister, he finds the position insufficient. I believe one day he will create a disturbance." Emperor Taizong responded, "Hou Junji is very talented and capable of serving in any position. It is not that I am unwilling to give him the highest post; it is just that it is not yet his turn. How can I distrust him and believe that he will commit treason?" After Hou was put to death, Emperor Taizong apologized to Li Daozong.