diff --git a/docs/development/current/main/phases/phase-286/C-2.1-pipeline-refactoring.md b/docs/development/current/main/phases/phase-286/C-2.1-pipeline-refactoring.md
new file mode 100644
index 00000000..c220656a
--- /dev/null
+++ b/docs/development/current/main/phases/phase-286/C-2.1-pipeline-refactoring.md
@@ -0,0 +1,216 @@
+# Phase 286C-2.1: 3-Stage Pipeline Refactoring
+
+## Goal
+Refactor `instruction_rewriter.rs` into a **3-stage pipeline** (Scan → Plan → Apply) to:
+1. Solve Rust borrow checker conflicts
+2. Clarify responsibilities (1 Box = 1 Question)
+3. Make code more maintainable and testable
+
+## Current Status: ✅ **Scaffolding Complete**
+
+### What's Done
+- ✅ Created 3 new module files with basic structure
+- ✅ Defined core data structures
+- ✅ Registered modules in `mod.rs`
+- ✅ Build passes (`cargo build --release`)
+
+### Files Created
+```
+src/mir/builder/control_flow/joinir/merge/rewriter/
+├── scan_box.rs       # Stage 1: Read-only scanning
+├── plan_box.rs       # Stage 2: Pure transformation
+└── apply_box.rs      # Stage 3: Builder mutation only
+```
+
+## The 3 Stages
+
+### Stage 1: Scan (Read-Only)
+**File**: `scan_box.rs`
+**Responsibility**: "What needs to be rewritten?"
+
+- **Input**: `&MirFunction`, `&JoinInlineBoundary`, `&RewriteContext`
+- **Output**: `RewritePlan` (describes WHAT to do)
+- **Key**: Does NOT touch `MirBuilder`
+
+**Data Structures**:
+```rust
+pub struct RewritePlan {
+    pub tail_calls: Vec<TailCallRewrite>,
+    pub return_conversions: Vec<ReturnConversion>,
+    pub phi_adjustments: Vec<PhiAdjustment>,
+    pub parameter_bindings: Vec<ParameterBinding>,
+}
+```
+
+**What it does**:
+- Identify tail calls to rewrite
+- Find return instructions to convert
+- Detect PHI adjustments needed
+- Collect parameter binding requirements
+
+### Stage 2: Plan (Pure Transformation)
+**File**: `plan_box.rs`
+**Responsibility**: "How should the MIR look after rewriting?"
+
+- **Input**: `RewritePlan`
+- **Output**: `RewrittenBlocks` (new blocks, PHI tables, remapping tables)
+- **Key**: Can update `RewriteContext` but does NOT touch builder
+
+**Data Structures**:
+```rust
+pub struct RewrittenBlocks {
+    pub new_blocks: Vec<BasicBlock>,
+    pub block_replacements: BTreeMap<BasicBlockId, BasicBlock>,
+    pub phi_inputs: Vec<(BasicBlockId, ValueId)>,
+    pub carrier_inputs: BTreeMap<String, Vec<(BasicBlockId, ValueId)>>,
+}
+```
+
+**What it does**:
+- Generate new basic blocks based on plan
+- Create PHI input mappings
+- Prepare parameter binding instructions
+- Build block ID remapping tables
+
+### Stage 3: Apply (Builder Mutation Only)
+**File**: `apply_box.rs`
+**Responsibility**: "Put the new MIR into the builder"
+
+- **Input**: `&mut MirBuilder`, `RewrittenBlocks`
+- **Output**: Merge result reflected in builder
+- **Key**: ONLY adds/replaces blocks in builder
+
+**What it does**:
+- Add new blocks to MirBuilder
+- Replace modified blocks
+- Update function metadata
+
+## Why This Approach Works
+
+**The Borrow Checker Problem**:
+- Currently: Mutating `MirBuilder` while updating `RewriteContext` causes conflicts
+- Solution: **Separate "read", "plan", and "apply" into distinct time windows**
+
+**Borrow Lifecycle**:
+```rust
+// Stage 1: Read-Only (immutable borrow)
+let plan = scan(&mir_function, &boundary, &ctx);
+
+// Stage 2: Pure (no builder borrow)
+let blocks = plan_transform(plan, &mut ctx);
+
+// Stage 3: Mutation (mutable borrow, no conflicts)
+apply(&mut builder, blocks);
+```
+
+## Implementation Strategy (Incremental)
+
+### ✅ Step 0: Scaffolding (DONE)
+- [x] Create 3 files with basic structure
+- [x] Define data structures
+- [x] Register modules
+- [x] Test build
+
+### 🔄 Step 1: Split within same file (NEXT)
+Create 3 functions in `instruction_rewriter.rs`:
+```rust
+fn scan(...) -> RewritePlan { ... }
+fn plan(plan: RewritePlan) -> RewrittenBlocks { ... }
+fn apply(builder: &mut MirBuilder, blocks: RewrittenBlocks) { ... }
+```
+
+Refactor `merge_and_rewrite()` to:
+```rust
+pub fn merge_and_rewrite(...) -> Result<MergeResult, String> {
+    let plan = scan(...);
+    let blocks = plan(plan);
+    apply(builder, blocks)?;
+    // ... existing post-processing ...
+}
+```
+
+**Test**: `cargo build --release` + quick smoke tests
+
+### 📦 Step 2: Extract to separate files
+- Move `scan()` → `scan_box.rs`
+- Move `plan()` → `plan_box.rs`
+- Move `apply()` → `apply_box.rs`
+
+**Test**: `cargo build --release` + quick smoke tests
+
+### 🔗 Step 3: Merge existing helper boxes
+- Integrate `InstructionFilterBox`, `TailCallDetectorBox` → into `ScanBox`
+- Integrate `ParameterBindingBox`, `ReturnConverterBox` → into `PlanBox`
+
+**Test**: `cargo build --release` + quick smoke tests
+
+## Current Implementation State
+
+### ScanBox (`scan_box.rs`)
+**Status**: Scaffolding only
+- ✅ Data structures defined
+- ⏳ Logic stub (returns empty result)
+- ⏳ Needs implementation
+
+**Next**: Implement `scan_block()` logic
+
+### PlanBox (`plan_box.rs`)
+**Status**: Scaffolding only
+- ✅ Data structures defined
+- ⏳ Logic stub (returns empty result)
+- ⏳ Needs implementation
+
+**Next**: Implement `transform()` logic
+
+### ApplyBox (`apply_box.rs`)
+**Status**: Basic implementation
+- ✅ Data structures defined
+- ✅ Basic `apply()` implementation (adds/replaces blocks)
+- ⏳ Needs integration with full pipeline
+
+**Next**: Test with real data
+
+## Testing Strategy
+
+### Unit Tests
+Each Box should have tests:
+- `scan_box.rs`: Test block scanning logic
+- `plan_box.rs`: Test plan → blocks transformation
+- `apply_box.rs`: Test builder mutation
+
+### Integration Tests
+- Test full pipeline: scan → plan → apply
+- Compare output with current `merge_and_rewrite()` (should be identical)
+
+### Smoke Tests
+Use existing smoke tests after each step:
+- `tools/smokes/v2/run.sh --profile quick`
+- No new failures beyond known issues
+
+## Success Criteria
+
+1. ✅ `merge_and_rewrite()` becomes ~100-200 line orchestrator
+2. ✅ `cargo build --release` passes at each step
+3. ⏳ Quick smoke tests maintain (no new failures)
+4. ⏳ Borrow checker conflicts resolved
+5. ⏳ Zero functionality changes (pure refactoring)
+
+## Important Notes
+
+- **Incremental steps** - test after each change
+- **Preserve all functionality** - this is refactoring, not rewriting
+- **Use RewriteContext from Phase 286C-2** - already committed
+- **Read current code first** - understand actual structure before changing
+
+## Next Steps
+
+1. **Implement Step 1**: Split `merge_and_rewrite()` into 3 functions within same file
+2. **Test extensively**: Ensure no behavioral changes
+3. **Document edge cases**: Identify any special handling needed
+4. **Proceed to Step 2**: Extract to separate files only after Step 1 works
+
+## References
+
+- **Original file**: `src/mir/builder/control_flow/joinir/merge/instruction_rewriter.rs` (1422 lines)
+- **RewriteContext**: `src/mir/builder/control_flow/joinir/merge/rewriter/rewrite_context.rs`
+- **Existing helper boxes**: `instruction_filter_box.rs`, `parameter_binding_box.rs`, etc.
diff --git a/src/mir/builder/control_flow/joinir/merge/rewriter/apply_box.rs b/src/mir/builder/control_flow/joinir/merge/rewriter/apply_box.rs
new file mode 100644
index 00000000..d5af1436
--- /dev/null
+++ b/src/mir/builder/control_flow/joinir/merge/rewriter/apply_box.rs
@@ -0,0 +1,63 @@
+//! ApplyBox: Builder mutation only (RewrittenBlocks → MirBuilder)
+//!
+//! Phase 286C-2.1: Third stage of 3-stage pipeline (Scan → Plan → Apply)
+//! Adds/replaces blocks in MirBuilder WITHOUT reading/analyzing.
+
+use crate::mir::builder::MirBuilder;
+use crate::mir::{BasicBlock, BasicBlockId};
+
+use super::plan_box::RewrittenBlocks;
+
+/// ApplyBox: Builder mutation only
+pub struct ApplyBox;
+
+impl ApplyBox {
+    /// Apply rewritten blocks to the MirBuilder
+    ///
+    /// This is the ONLY stage that mutates the builder.
+    /// It doesn't analyze or plan - just adds/replaces blocks.
+    ///
+    /// # Arguments
+    /// * `builder` - The MirBuilder to mutate
+    /// * `blocks` - The rewritten blocks from PlanBox
+    ///
+    /// # Returns
+    /// * Result indicating success or failure
+    pub fn apply(builder: &mut MirBuilder, blocks: RewrittenBlocks) -> Result<(), String> {
+        // Add new blocks
+        if let Some(ref mut current_func) = builder.scope_ctx.current_function {
+            for block in blocks.new_blocks {
+                current_func.add_block(block);
+            }
+
+            // Replace existing blocks
+            for (block_id, new_block) in blocks.block_replacements {
+                current_func.blocks.insert(block_id, new_block);
+            }
+        }
+
+        Ok(())
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::mir::builder::MirBuilder;
+    use std::collections::BTreeMap;
+
+    #[test]
+    fn test_apply_box_basic() {
+        // Basic smoke test
+        let mut builder = MirBuilder::new();
+        let blocks = RewrittenBlocks {
+            new_blocks: Vec::new(),
+            block_replacements: BTreeMap::new(),
+            phi_inputs: Vec::new(),
+            carrier_inputs: BTreeMap::new(),
+        };
+
+        let result = ApplyBox::apply(&mut builder, blocks);
+        assert!(result.is_ok());
+    }
+}
diff --git a/src/mir/builder/control_flow/joinir/merge/rewriter/mod.rs b/src/mir/builder/control_flow/joinir/merge/rewriter/mod.rs
index 46b5c26e..abcda812 100644
--- a/src/mir/builder/control_flow/joinir/merge/rewriter/mod.rs
+++ b/src/mir/builder/control_flow/joinir/merge/rewriter/mod.rs
@@ -43,6 +43,11 @@ pub(super) mod tail_call_detector_box; // Phase 286C-2 Step 2: Tail call detecti
 pub(super) mod terminator; // Phase 260 P0.1 Step 5: Terminator remapping extracted ✅
 pub(super) mod type_propagation; // Phase 260 P0.1 Step 4: Type propagation extracted ✅
 
+// Phase 286C-2.1: 3-stage pipeline (Scan → Plan → Apply) ✅
+pub(super) mod scan_box; // Stage 1: Read-only scanning for rewrite planning
+pub(super) mod plan_box; // Stage 2: Pure transformation (scan → blocks)
+pub(super) mod apply_box; // Stage 3: Builder mutation only
+
 // Re-export public API
  // Phase 260 P0.1 Step 3: From helpers ✅
 pub(super) use super::instruction_rewriter::merge_and_rewrite; // Still in parent (TODO: extract)
diff --git a/src/mir/builder/control_flow/joinir/merge/rewriter/plan_box.rs b/src/mir/builder/control_flow/joinir/merge/rewriter/plan_box.rs
new file mode 100644
index 00000000..a27dc17c
--- /dev/null
+++ b/src/mir/builder/control_flow/joinir/merge/rewriter/plan_box.rs
@@ -0,0 +1,70 @@
+//! PlanBox: Pure transformation (Scan → RewrittenBlocks)
+//!
+//! Phase 286C-2.1: Second stage of 3-stage pipeline (Scan → Plan → Apply)
+//! Generates new blocks and mappings WITHOUT touching the builder.
+
+use crate::mir::{BasicBlock, BasicBlockId, ValueId};
+use std::collections::BTreeMap;
+
+use super::scan_box::RewritePlan;
+
+/// Rewritten blocks: New blocks, PHI inputs, carrier inputs (ready to apply)
+#[derive(Debug, Clone)]
+pub struct RewrittenBlocks {
+    /// New blocks to add to the builder
+    pub new_blocks: Vec<BasicBlock>,
+
+    /// Block replacements: Map<block_id, new_block>
+    pub block_replacements: BTreeMap<BasicBlockId, BasicBlock>,
+
+    /// PHI inputs for exit block: Vec<(from_block, value)>
+    pub phi_inputs: Vec<(BasicBlockId, ValueId)>,
+
+    /// Carrier inputs: Map<carrier_name, Vec<(from_block, value)>>
+    pub carrier_inputs: BTreeMap<String, Vec<(BasicBlockId, ValueId)>>,
+}
+
+/// PlanBox: Pure transformation from RewritePlan to RewrittenBlocks
+pub struct PlanBox;
+
+impl PlanBox {
+    /// Transform a RewritePlan into RewrittenBlocks
+    ///
+    /// This is a PURE transformation - no builder mutation, no side effects.
+    /// Can update RewriteContext but does NOT touch MirBuilder.
+    ///
+    /// # Arguments
+    /// * `plan` - The rewrite plan from ScanBox
+    ///
+    /// # Returns
+    /// * RewrittenBlocks ready to be applied to the builder
+    pub fn transform(_plan: RewritePlan) -> RewrittenBlocks {
+        // TODO: Implement transformation logic
+        // For now, return empty result
+        RewrittenBlocks {
+            new_blocks: Vec::new(),
+            block_replacements: BTreeMap::new(),
+            phi_inputs: Vec::new(),
+            carrier_inputs: BTreeMap::new(),
+        }
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_plan_box_basic() {
+        // Basic smoke test
+        let plan = RewritePlan {
+            tail_calls: Vec::new(),
+            return_conversions: Vec::new(),
+            phi_adjustments: Vec::new(),
+            parameter_bindings: Vec::new(),
+        };
+
+        let blocks = PlanBox::transform(plan);
+        assert!(blocks.new_blocks.is_empty());
+    }
+}
diff --git a/src/mir/builder/control_flow/joinir/merge/rewriter/scan_box.rs b/src/mir/builder/control_flow/joinir/merge/rewriter/scan_box.rs
new file mode 100644
index 00000000..d8c3e992
--- /dev/null
+++ b/src/mir/builder/control_flow/joinir/merge/rewriter/scan_box.rs
@@ -0,0 +1,162 @@
+//! ScanBox: Read-only scanning for rewrite planning
+//!
+//! Phase 286C-2.1: First stage of 3-stage pipeline (Scan → Plan → Apply)
+//! Identifies what needs to be rewritten WITHOUT mutating any state.
+
+use crate::mir::{BasicBlock, BasicBlockId, MirFunction, MirInstruction, ValueId};
+use std::collections::BTreeSet;
+
+/// Rewrite plan: Describes WHAT to do (doesn't touch instructions yet)
+#[derive(Debug, Clone)]
+pub struct RewritePlan {
+    /// Tail calls to be converted to parameter bindings + Jump
+    pub tail_calls: Vec<TailCallRewrite>,
+
+    /// Return instructions to convert to Jump to exit block
+    pub return_conversions: Vec<ReturnConversion>,
+
+    /// PHI adjustments needed (currently empty, for future use)
+    pub phi_adjustments: Vec<PhiAdjustment>,
+
+    /// Parameter bindings to generate for tail calls
+    pub parameter_bindings: Vec<ParameterBinding>,
+}
+
+/// Information about a tail call to rewrite
+#[derive(Debug, Clone)]
+pub struct TailCallRewrite {
+    /// Block containing the tail call
+    pub block_id: BasicBlockId,
+
+    /// Target function name
+    pub target_func_name: String,
+
+    /// Target block (entry block of called function)
+    pub target_block: BasicBlockId,
+
+    /// Remapped arguments to pass
+    pub args: Vec<ValueId>,
+
+    /// Whether this is a recursive call (same function)
+    pub is_recursive: bool,
+
+    /// Whether this is a continuation call (k_exit, etc.)
+    pub is_continuation: bool,
+
+    /// Whether the target is the loop entry function
+    pub is_loop_entry: bool,
+}
+
+/// Information about a Return instruction to convert
+#[derive(Debug, Clone)]
+pub struct ReturnConversion {
+    /// Block containing the Return
+    pub block_id: BasicBlockId,
+
+    /// Return value (if any)
+    pub return_value: Option<ValueId>,
+
+    /// Whether this has exit edge args
+    pub has_exit_edge_args: bool,
+
+    /// Whether to keep Return (non-skippable continuation)
+    pub should_keep_return: bool,
+}
+
+/// PHI adjustment (placeholder for future use)
+#[derive(Debug, Clone)]
+pub struct PhiAdjustment {
+    /// Block containing the PHI
+    pub block_id: BasicBlockId,
+
+    /// PHI destination
+    pub phi_dst: ValueId,
+}
+
+/// Parameter binding to generate
+#[derive(Debug, Clone)]
+pub struct ParameterBinding {
+    /// Block to insert the binding into
+    pub block_id: BasicBlockId,
+
+    /// Destination ValueId (parameter)
+    pub dst: ValueId,
+
+    /// Source ValueId (argument)
+    pub src: ValueId,
+}
+
+/// ScanBox: Read-only scanning for rewrite planning
+pub struct ScanBox;
+
+impl ScanBox {
+    /// Scan a block to identify rewrite operations needed
+    ///
+    /// This is a READ-ONLY operation - it doesn't mutate any state,
+    /// just analyzes what needs to be done.
+    ///
+    /// # Arguments
+    /// * `block` - The block to scan
+    /// * `block_id` - The block's ID
+    /// * `func_name` - The function containing this block
+    /// * Additional context parameters (TODO: consolidate into ScanContext)
+    ///
+    /// # Returns
+    /// * Instructions to skip, tail calls found, returns to convert, etc.
+    pub fn scan_block(
+        block: &BasicBlock,
+        block_id: BasicBlockId,
+        _func_name: &str,
+    ) -> BlockScanResult {
+        let mut skip_instructions = BTreeSet::new();
+        let mut found_tail_call = false;
+
+        // Scan instructions for tail calls, returns, etc.
+        for (idx, inst) in block.instructions.iter().enumerate() {
+            match inst {
+                MirInstruction::Call { .. } => {
+                    // Detect tail calls
+                    // TODO: Implement tail call detection logic
+                    found_tail_call = false; // Placeholder
+                }
+                MirInstruction::Return { .. } => {
+                    // Mark return for conversion
+                    // TODO: Implement return conversion detection
+                }
+                _ => {}
+            }
+        }
+
+        BlockScanResult {
+            skip_instructions,
+            found_tail_call,
+            tail_call_target: None,
+        }
+    }
+}
+
+/// Result of scanning a single block
+#[derive(Debug, Clone)]
+pub struct BlockScanResult {
+    /// Instruction indices to skip during rewriting
+    pub skip_instructions: BTreeSet<usize>,
+
+    /// Whether a tail call was found
+    pub found_tail_call: bool,
+
+    /// Tail call target (if found)
+    pub tail_call_target: Option<(BasicBlockId, Vec<ValueId>)>,
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_scan_box_basic() {
+        // Basic smoke test - will expand with real logic
+        let block = BasicBlock::new(BasicBlockId(0));
+        let result = ScanBox::scan_block(&block, BasicBlockId(0), "test_func");
+        assert!(!result.found_tail_call);
+    }
+}