This paper presents an argument for how second language acquisition (SLA) research should be carried out if a researcher is genuinely interested in learner grammar (i.e., knowledge of language), its acquisition and use. SLA research has expanded greatly over many years and currently spans many subfields, but researchers share one main goal: to describe and explain second language learners' knowledge and behavior in a broad sense. After presenting important insights from Doughty and Long (2003), who discuss relations between SLA research and language teaching, we divide these subfields into three areas following Wakabayashi (2003) and contend that investigating learners' linguistic systems is the core area of SLA research. We will illustrate the importance of linguistic theory-based research with data concerning 3rd person singular -s in English. It will be argued that SLA studies need a rigorous descriptive tool (i.e., a theoretical framework) to describe and explain the system underlying learners' behavior in their use of second languages.