This study investigated the effects of scaffolding in Algebra on the Problem-solving performance, mathematics performance, sense of agency, and anxiety of second year students. It employed the mixed methods research design, quasi-experimental matching only pretest-posttest design and utilized three(3) intact sections with 52 matched-paired second year students in which 31 pairs were from Dona Montserant Lopez Memorial High School, Silay City, and 21 pairs were from Rafael B. Lacson Memorial High School, Talisay City. These students were enrolled in the first semester of SY 2012-2013 and their sections were randomly assigned to the three scaffolding groups namely:maximum, minimum, and without teacher's assistance by fish bowl method. For the quantitative part, this study utilized four validated and reliable instruments namely: Problem-Solving performance Test (PSPT), Mathematics Performance Test (MPT), Sense of Agency Questionnaire (SAQ), and Mathematics Anxiety Questionnaire(MAQ). The qualitative data were gathered using the student's journal, interviewed schedule, and observation guide. Results revealed that before the intervention, student's problem-solving performance was developing, heir mathematics performance was low, their sense of agency was generally high, and their mathematics anxiety was in the average level. After the intervention, the student's problem-solving performance was generally in the accomplished level, except for the without-assistance group that remained as developing, their mathematics performance elevated to average level, their sense of agency was generally high, except in the minimum assistance group that remained in the average level, and their mathematics anxiety level remained in the average level. ANOVA results revealed significant difference i the problem solving performance of the students, with the without-assistance group having a better PSP compared to the other two scaffolding groups but became significantly lower after the intervention. No significant difference existed in the mathematics performance, sense of agency, ad mathematics anxiety of the students before the intervention but the without-assistance group exhibited significantly higher sense of agency and mathematics anxiety after the intervention. Significant differences existed in the mean gain of scores between Problem-Solving Performance(PSP) and mathematics anxiety of the students. Both the maximum- and minimum assistance groups had higher PSP than the without-assistance group. The minimum scaffolding group had a higher mathematics anxiety than the maximum-assistance group. However no significant differences existed in the mean gain scores of mathematics performance and sense of agency of the students. Students approached their problem-solving tasks by constantly reading the problems to ensure understanding of the problems, planning a strategy on how to work out the problems, and checking the answers for its worth and plausibility. Promoting collaboration and teamwork and innovativeness were among the favorable and worthwhile effects of problem-solving activities on the student's mathematics performance while frustration in doing problem solving was ts adverse effect. Developing self-confidence in doing problem solving to improve mathematics performance confirmed student's high sense of agency. Problem-solving activities developed disappointment and anxiety among the students, yet sparked learning and brought success to the students. The HELP (Humane, Emergent, Love, Perspective) theory was introduced to help both the student's and the teachers in doing problem-solving activities.