In 2020, Cook redshirted and appeared in three games. Cook recorded 72 yards passing and one touchdown.[3] Cook entered the 2021 season as the backup to Connor Bazelak. After Bazelak struggled and eventually got injured, Cook received his first major playing time against Georgia, in which Cook threw for 78 yards in a 43–6 loss.[4] Cook made his first career start against Army in the 2021 Armed Forces Bowl, in which Cook tallied 238 passing yards and a touchdown while rushing for 53 yards and a touchdown.[5] Entering the 2022 season, Cook was named the starting quarterback.[6][7] Cook led Missouri to a 2–2 start including a three touchdown performance against Abilene Christian.[8] Cook then led Missouri to a 22–12 lead over No. 1 Georgia in the fourth quarter. Despite this, Georgia scored 14 unanswered points to win 26–22. Cook finished the game with 192 yards and a touchdown.[9] Cook finished the season throwing for 2,739 yards, 14 touchdowns, and seven interceptions, while also rushing for 585 yards and six touchdowns, leading Missouri to the 2022 Gasparilla Bowl.[10]
2023
Entering the 2023 season, Cook competed with Jake Garcia and Sam Horn for Missouri's starting quarterback job, with Cook eventually being named the starter.[11][12] In week three against No. 15 Kansas State, he threw for 356 yards and contributed three total touchdowns in a 30–27 upset victory.[13][14] Against Vanderbilt, Cook threw for a then career-high, 395 yards and four touchdowns, in a 38–21 rout.[15] During the game, he set an SEC record for most consecutive passes without an interception, overtaking the previous record from former Kentucky quarterback Andre' Woodson.[16] Cook led Missouri to a 5–0 record before a matchup with No. 23 LSU, where he recorded a career-high 411 passing yards and threw for two touchdowns.[17] Despite his efforts, LSU was victorious 49–39. The following week, Cook helped Missouri bounce back with a 38–21 victory over No. 24 Kentucky, contributing two total touchdowns.[18] Against South Carolina, he threw for 198 yards and totaled two touchdowns, leading Missouri to a 7–1 record, the team's best record through eight games since 2013.[19]
During the 2023 regular season, Cook led Missouri to a 10–2 record and an appearance in the 2023 Cotton Bowl Classic, finishing the year with 20 passing touchdowns, 3,189 passing yards, and eight rushing touchdowns.[20] In the Cotton Bowl Classic, Cook threw for 128 yards and a touchdown, leading Missouri to a 14–3 victory over Ohio State.[21][22] As a result of his performance, he was named the game's offensive MVP.[23] Following the game, he announced that he would return to Missouri the following season after finishing the 2023 season throwing for 3,317 yards, rushing for 319 yards, and totaling 29 total touchdowns.[24]
2024
In the season opener against Murray State, Cook threw for 218 yards and totaled two touchdowns, one rushing and one passing, in a 51–0 rout.[25] Against Auburn, he suffered an injury on the opening drive of the game and was taken to the hospital to have an MRI exam on his ankle. Unexpected to return to the game, Cook came back into the game with Missouri trailing 17–6 near the end of the third quarter. He then led the Tigers to two touchdown drives, resulting in a 21–17 Missouri victory. Cook finished the game with 194 yards passing.[26][27] The following week, he gained the start against No. 15 Alabama, despite not being able to practice due to the ankle injury he sustained against Auburn.[28] Cook exited the game after sustaining a wrist injury, finishing the game with 30 passing yards.[29][30] Dealing with the wrist and ankle injuries, he was sidelined against Oklahoma, marking the end of 35 consecutive starts for Cook.[31][32]