3D instance segmentation aims to predict a set of object instances in a scene and represent them as binary foreground masks with corresponding semantic labels. Currently, transformer-based methods are gaining increasing attention due to their elegant pipelines, reduced manual selection of geometric properties, and superior performance. However, transformer-based methods fail to simultaneously maintain strong position and content information during query initialization. Additionally, due to supervision at each decoder layer, there exists a phenomenon of object disappearance with the deepening of layers. To overcome these hurdles, we introduce Beyond the Final Layer: Hierarchical Query Fusion Transformer with Agent-Interpolation Initialization for 3D Instance Segmentation (BFL). Specifically, an Agent-Interpolation Initialization Module is designed to generate resilient queries capable of achieving a balance between foreground coverage and content learning. Additionally, a Hierarchical Query Fusion Decoder is designed to retain low overlap queries, mitigating the decrease in recall with the deepening of layers. Extensive experiments on ScanNetV2, ScanNet200, ScanNet++ and S3DIS datasets demonstrate the superior performance of BFL.