piRNAs are required to silence transposons in the germline to maintain genome stability and transmission of an intact genome to the next generation. In Drosophila, biogenesis of these small RNAs occurs in three distinct compartments: the nucleus, perinuclear nuage, and the outer mitochondria membrane. My thesis focuses on how genomic instability via transposon-initiated DNA damage and heat stress impact piRNA pathway organization and function. We show that activation of Chk2, a Checkpoint kinase required for DNA damage signaling, disrupts nuage composition and this complicates piRNA mutant phenotypes. Stripping away DNA damage signaling in piRNA mutants provided new insight into how the nuclear piRNA proteins organize the cytoplasmic nuage. Additionally, we found that localization of key components to nuage is dispensable for piRNA production and transposon silencing. piRNA pathway proteins are not only susceptible to genomic instability, but also sensitive to heat shock. Rhino is a core component of the nuclear piRNA pathway and displays drastic localization changes upon heat shock that recovers with time. piRNAs have been proposed to help localize Rhino and heat stress provided a unique platform to test this model. We show that Rhino recovery after heat shock does not require Piwi, the sole nuclear protein bound to piRNAs, and this points to piRNAs having a less significant role in Rhino localization. Taken together, we show how different types of stress can modulate the piRNA pathway in unexpected manners.