The purpose of this quasi-experimental, mixed-methods study was to address the gap in understanding regarding second language (L2) comprehension of stories by using a taxonomical approach based on Anderson and Krathwohl's (2001) revised taxonomy that includes multiple levels of cognitive processing to provide insight into L2 learners' depth of comprehension. In addition, this study investigated the impact of reading, reading-while-listening, and listening input modalities as it applies to story comprehension. L2 comprehension studies where all three of these input methods are compared are scarce. Finally, the effect of input type on learner affect--task enjoyment and perceived task difficulty--was explored. No previous mixed methods L2 comprehension studies have accounted for all the above variables. The participants (N = 134, 85 male and 49 female students) of the quantitative aspect of this study were Japanese university students who were streamed into the university's reading and writing or listening and speaking classes. At the time of the study, they were first- and second-year, non-English majors taking English courses as a general university requirement at a private university in western Japan. Participants from six intact classes were tasked with reading two chapters, reading-while-listening to two chapters, and listening to two chapters of a six-chapter graded reader. Using a Latin squares design, each class received a different input method at the beginning, middle, and end of each story. Three 250-headword, CEFR level 1 short stories of similar lengths from the Oxford Dominos series were used for each participant group. The participants received short, bilingual vocabulary lists for vocabulary that fell outside of the first 1,000 BNC/COCA high-frequency words of English prior to receiving each story. After finishing two chapters using one of the above three input modalities, the texts were returned to me and the participants answered bilingual remember questions of the factual recall subtype, understand questions of the inferencing subtype, and evaluate questions of the judging or critique subtypes based on Anderson and Krathwohl's (2001) revised taxonomy. They then rated task difficulty and task enjoyment. Both the remember and understand questions were four-option multiple-choice questions, while the evaluate questions required written responses in Japanese. To ensure task time equivalency, the participants received two repeated listenings at approximately 138-157 words per minute (WPM) for the reading-while-listening and listening tasks. The participants were given approximately 18 minutes to complete each of the three chapters and 10 minutes to answer questions. Using data from Rasch person measures, a series of mixed model analyses were used to assess the participants' performances on remember, understand, and evaluate comprehension questions as mediated by input modality. Input modality--reading, reading-while-listening, and listening--was the independent variable, while the remember, understand, and evaluate comprehension questions made up the dependent variables. The New Vocabulary Levels Test (NVLT) scores were used as the covariate. The results indicated that the participants scored higher overall on the remember questions (M = 54.06) than on the understand questions (M = 52.62) or the evaluate questions (M = 49.31). Regarding task-type findings, the reading and reading-while-listening tasks resulted in significantly better comprehension than listening tasks but were not significantly different from one another for remember and understand comprehension questions. For evaluate comprehension questions, all three inputs resulted in significantly different comprehension with reading resulting in the highest comprehension, followed by reading-while-listening, and then listening. The NVLT was a significant predictor of comprehension at all levels, but it had small R[superscript 2] values. Listening tasks resulted in significantly lower scores than both the reading and reading-while-listening input conditions for all three comprehension levels. In addition, the participants rated that they perceived the reading-while-listening and listening tasks to be more difficult than reading tasks. Reading and reading-while-listening tasks were rated as more enjoyable than listening tasks. After the quantitative data were gathered, qualitative interviews were conducted to better investigate the research hypotheses and the quantitative findings. Six participants were from the same university as the quantitative sample (N = 6, 1 male and 5 female) and four participants were from another nearby university (N = 4, 3 male and 1 female). These participants completed the second text, "The Bottle Imp" (Stevenson, 2008), by reading Chapters 1-2, reading-while-listening to Chapters 3-4, and listening to Chapters 5-6 in the same manner as the quantitative groups except they did not follow a Latin squares design. After the completion of each two-chapter section, the participants provided verbal recalls to ensure that they correctly performed the task and to gain insight into what was understood from the text. Next, they answered comprehension questions and gave task enjoyment and task difficulty ratings. Finally, the participants answered interview questions designed to clarify their thoughts about the tasks. Verbal recalls and interviews were audio-recorded, and the interviews were transcribed and coded based on Saldana (2016). [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://bibliotheek.ehb.be:2222/en-US/products/dissertations/individuals.shtml.]