Adolescents globally are vulnerable to mental disorders, injuries and unhealthy lifestyle choices, and this is heightened in young people who live in adversity. Early intervention programmes for adolescents can promote mental health, prevent mental disorders, and prevent risky behaviours and other unhealthy lifestyle choices. These programmes have the potential to make positive contributions to adolescents' health, and to their health in later life. Since about 80% of young adolescents globally are in school, intervention programmes delivered in the school setting could reach a large proportion of adolescents. We reviewed the evidence for school-based intervention programmes and found that most programmes come from high-income countries, and focus on one issue only, such as tobacco or alcohol use, or violence. Since many risk factors for poor mental and physical health, such as alcohol use and risky sexual behaviour, occur together, a programme targeting a range of factors could be more effective and more cost-effective. Such programmes may be more attractive to policymakers in low resourced settings. However, classroom-based programmes alone are unlikely to impact whole schools and sustain improved health benefits. Combining broader school climate and classroom-based programmes has been effective in reducing bullying and mental health symptoms in previous studies. The aim of this study is to address the evidence gap by developing and adapting a multilevel, gender-sensitive school intervention programme in low- and middle-income countries (LMICs) targeting a range of negative mental and physical health outcomes by promoting positive mental health; preventing mental disorders (specifically, depression and anxiety); and preventing a range of risk behaviours in young at-risk adolescents. We propose to develop the programme (Project HASHTAG) in two LMICs, South Africa and Nepal, co-producing two strategies: a broader school climate and classroom-based programme with adolescents, parents, teachers and school managers. For the first strategy, a school-level assessment, planning and action process, Thriving Environment in Schools (TES), will be conducted to improve school climate. School climate is defined as staff and students' perceptions of the school environment, which is influenced by the school organisational structure, relationships among staff and students, and their attitudes and behaviours. School climate improvement strategies support the role of classroom-based interventions by boosting commitment from teachers, staff and students, and by reinforcing content of classroom-based strategies. For the second strategy, adolescents ages 11-12 will participate in a group programme known as Thrive Together (TT), to equip them with skills identified in the evidence review as being effective in promoting mental health, and preventing mental health problems and risky behaviours. To develop and test these strategies, Project HASHTAG will comprise two phases. In the development phase we will interview stakeholders, and observe school environments and staff-student interactions to: (i) develop an outline of TES and (ii) gather suggestions for TT, with adolescents, parents, teachers, and other stakeholders in two schools per country. These suggestions will inform the work of an intervention development group in producing a TT programme draft. In the feasibility phase, we will assess the students before and after the TES and TT strategies are implemented in four schools per country using questionnaires. We will assess whether the questionnaires capture the necessary information on school climate, mental health and risky behaviours. We will also evaluate whether the processes needed to implement the programme work well. After programme completion, we will interview students and stakeholders about their opinions of the programme and whether it is feasible to implement in schools, and what will hinder or help this implementation.