diff --git a/template.html b/template.html
index cebcfe1..93f30e5 100644
--- a/template.html
+++ b/template.html
@@ -562,6 +562,232 @@
       color: var(--text-color);
     }
 
+    /* ========================================
+       PLOT COMPARISON OVERLAY
+       ======================================== */
+    .comparison-overlay {
+      position: fixed;
+      top: 0;
+      left: 0;
+      width: 100%;
+      height: 100%;
+      background: rgba(0, 0, 0, 0.9);
+      z-index: 2000;
+      display: none;
+      backdrop-filter: blur(4px);
+    }
+    
+    .comparison-overlay.open {
+      display: flex;
+      align-items: center;
+      justify-content: center;
+    }
+    
+    .comparison-container {
+      width: 95%;
+      height: 90%;
+      background: var(--bg-color);
+      border-radius: 12px;
+      padding: 1.5rem;
+      display: flex;
+      flex-direction: column;
+      position: relative;
+      box-shadow: 0 10px 30px rgba(0,0,0,0.5);
+    }
+    
+    .comparison-header {
+      display: flex;
+      justify-content: space-between;
+      align-items: center;
+      margin-bottom: 1rem;
+      padding-bottom: 1rem;
+      border-bottom: 1px solid var(--border-color);
+    }
+    
+    .comparison-title {
+      font-size: 1.5rem;
+      font-weight: 600;
+      color: var(--text-color);
+      margin: 0;
+    }
+    
+    .comparison-close {
+      background: var(--button-bg);
+      color: white;
+      border: none;
+      border-radius: 50%;
+      width: 40px;
+      height: 40px;
+      font-size: 1.2rem;
+      cursor: pointer;
+      transition: all 0.2s ease;
+    }
+    
+    .comparison-close:hover {
+      background: var(--button-hover);
+      transform: scale(1.1);
+    }
+    
+    .comparison-content {
+      flex: 1;
+      display: flex;
+      gap: 1rem;
+      overflow: hidden;
+    }
+    
+    .comparison-panel {
+      flex: 1;
+      display: flex;
+      flex-direction: column;
+      background: var(--card-bg);
+      border: 1px solid var(--border-color);
+      border-radius: 8px;
+      overflow: hidden;
+    }
+    
+    .comparison-panel-header {
+      background: var(--tree-bg);
+      padding: 0.8rem 1rem;
+      border-bottom: 1px solid var(--border-color);
+      display: flex;
+      justify-content: space-between;
+      align-items: center;
+    }
+    
+    .comparison-panel-title {
+      font-weight: 600;
+      color: var(--text-color);
+      font-size: 1rem;
+    }
+    
+    .comparison-replace-btn {
+      background: var(--success-color);
+      color: white;
+      border: none;
+      padding: 0.4rem 0.8rem;
+      border-radius: 4px;
+      font-size: 0.85rem;
+      cursor: pointer;
+      transition: all 0.2s ease;
+    }
+    
+    .comparison-replace-btn:hover {
+      background: var(--success-hover);
+    }
+    
+    .comparison-panel-content {
+      flex: 1;
+      display: flex;
+      align-items: center;
+      justify-content: center;
+      padding: 1rem;
+      overflow: auto;
+    }
+    
+    .comparison-plot-container {
+      width: 100%;
+      height: 100%;
+      display: flex;
+      align-items: center;
+      justify-content: center;
+      position: relative;
+    }
+    
+    .comparison-plot {
+      max-width: 100%;
+      max-height: 100%;
+      border: 1px solid var(--border-color);
+      border-radius: 4px;
+      cursor: pointer;
+      transition: transform 0.2s ease;
+    }
+    
+    .comparison-plot:hover {
+      transform: scale(1.02);
+    }
+    
+    .comparison-placeholder {
+      width: 100%;
+      height: 300px;
+      border: 2px dashed var(--border-color);
+      border-radius: 8px;
+      display: flex;
+      align-items: center;
+      justify-content: center;
+      color: var(--breadcrumb-color);
+      font-size: 1.1rem;
+      cursor: pointer;
+      transition: all 0.2s ease;
+    }
+    
+    .comparison-placeholder:hover {
+      border-color: var(--button-bg);
+      color: var(--button-bg);
+    }
+    
+    .comparison-plot-info {
+      position: absolute;
+      bottom: 0.5rem;
+      left: 0.5rem;
+      right: 0.5rem;
+      background: rgba(0, 0, 0, 0.8);
+      color: white;
+      padding: 0.5rem;
+      border-radius: 4px;
+      font-size: 0.9rem;
+      opacity: 0;
+      transition: opacity 0.2s ease;
+    }
+    
+    .comparison-plot-container:hover .comparison-plot-info {
+      opacity: 1;
+    }
+
+    /* Plot selection mode */
+    .selecting-plots .grid-item {
+      cursor: pointer !important;
+      transition: all 0.2s ease;
+      position: relative;
+    }
+    
+    .selecting-plots .grid-item:hover {
+      transform: translateY(-4px);
+      box-shadow: 0 6px 20px rgba(0, 120, 212, 0.3);
+      border-color: var(--button-bg);
+    }
+    
+    .selecting-plots .grid-item::before {
+      content: '📊 Click to compare';
+      position: absolute;
+      top: 50%;
+      left: 50%;
+      transform: translate(-50%, -50%);
+      background: rgba(0, 120, 212, 0.95);
+      color: white;
+      padding: 0.5rem 1rem;
+      border-radius: 4px;
+      font-size: 0.9rem;
+      font-weight: 600;
+      opacity: 0;
+      transition: opacity 0.2s ease;
+      pointer-events: none;
+      z-index: 10;
+      white-space: nowrap;
+    }
+    
+    .selecting-plots .grid-item:hover::before {
+      opacity: 1;
+    }
+    
+    /* Ensure grid items are clickable in selection mode */
+    .selecting-plots .grid-item * {
+      pointer-events: none;
+    }
+    
+    .selecting-plots .grid-item {
+      pointer-events: auto;
+    }
+
     /* ========================================
        SUBDIRECTORIES LIST
        ======================================== */
@@ -690,6 +916,9 @@
     <button class="floating-btn sidebar-toggle" onclick="toggleSidebar()" id="sidebarToggle" title="Recent Plots (Ctrl+R)">
       📋
     </button>
+    <button class="floating-btn compare-toggle" onclick="app.toggleCompareMode()" id="compareToggle" title="Compare Plots (Ctrl+C)">
+      ⚖️
+    </button>
     <button class="floating-btn theme-toggle" onclick="toggleTheme()" id="themeToggle" title="Toggle Theme (Ctrl+T)">
       ☀️
     </button>
@@ -709,6 +938,10 @@
       <span>Recent plots</span>
       <span class="shortcut-key">Ctrl+R</span>
     </div>
+    <div class="shortcut-item">
+      <span>Compare plots</span>
+      <span class="shortcut-key">Ctrl+C</span>
+    </div>
     <div class="shortcut-item">
       <span>Refresh</span>
       <span class="shortcut-key">F5</span>
@@ -743,6 +976,44 @@
     </div>
   </div>
 
+  <!-- Plot Comparison Overlay -->
+  <div class="comparison-overlay" id="comparisonOverlay">
+    <div class="comparison-container">
+      <div class="comparison-header">
+        <h2 class="comparison-title">Plot Comparison</h2>
+        <button class="comparison-close" onclick="app.closeComparison()" title="Close Comparison (Esc)">×</button>
+      </div>
+      <div class="comparison-content">
+        <div class="comparison-panel">
+          <div class="comparison-panel-header">
+            <span class="comparison-panel-title" id="leftPlotTitle">Plot A</span>
+            <button class="comparison-replace-btn" onclick="app.replacePlot('left')" id="leftReplaceBtn">Replace</button>
+          </div>
+          <div class="comparison-panel-content">
+            <div class="comparison-plot-container" id="leftPlotContainer">
+              <div class="comparison-placeholder" onclick="app.selectPlotForComparison('left')">
+                📊 Click to select first plot
+              </div>
+            </div>
+          </div>
+        </div>
+        <div class="comparison-panel">
+          <div class="comparison-panel-header">
+            <span class="comparison-panel-title" id="rightPlotTitle">Plot B</span>
+            <button class="comparison-replace-btn" onclick="app.replacePlot('right')" id="rightReplaceBtn">Replace</button>
+          </div>
+          <div class="comparison-panel-content">
+            <div class="comparison-plot-container" id="rightPlotContainer">
+              <div class="comparison-placeholder" onclick="app.selectPlotForComparison('right')">
+                📊 Click to select second plot
+              </div>
+            </div>
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+
   <script>
     // ========================================
     // GALLERY APPLICATION CLASS
@@ -752,6 +1023,12 @@
         this.searchTimeout = null;
         this.SEARCH_DEBOUNCE_MS = {{ ui.search_debounce_ms|default(300) }};
         this.MAX_RECENT_PLOTS = {{ ui.max_recent_plots|default(20) }};
+        
+        // Comparison state
+        this.comparisonMode = false;
+        this.comparisonSlot = null; // 'left' or 'right'
+        this.plots = { left: null, right: null };
+        
         this.init();
       }
 
@@ -1444,6 +1721,11 @@
             this.toggleSidebar();
           }
           
+          if (e.ctrlKey && e.key === 'c') {
+            e.preventDefault();
+            this.toggleCompareMode();
+          }
+          
           if (e.ctrlKey && e.key === 't') {
             e.preventDefault();
             this.toggleTheme();
@@ -1460,10 +1742,32 @@
           }
           
           if (e.key === 'Escape') {
+            // If in plot selection mode, cancel it
+            if (this.comparisonSlot) {
+              // Find and remove instruction element
+              const instruction = document.getElementById('comparisonInstruction');
+              if (instruction) instruction.remove();
+              
+              // Reset grid item styles
+              const gridItems = document.querySelectorAll('.grid-item');
+              gridItems.forEach(item => {
+                item.style.cursor = '';
+                item.style.border = '';
+              });
+              
+              // Show overlay again
+              document.getElementById('comparisonOverlay').style.display = 'flex';
+              this.comparisonSlot = null;
+              return;
+            }
+            
             document.getElementById('searchResults').style.display = 'none';
             if (document.getElementById('sidebar').classList.contains('open')) {
               this.toggleSidebar();
             }
+            if (document.getElementById('comparisonOverlay').classList.contains('open')) {
+              this.hideComparisonOverlay();
+            }
             document.getElementById('shortcutsHelp').style.display = 'none';
           }
         });
@@ -1510,6 +1814,168 @@
           }, 3000);
         }
       }
+
+      /**
+       * Toggle comparison mode
+       */
+      toggleCompareMode() {
+        this.comparisonMode = !this.comparisonMode;
+        const compareBtn = document.getElementById('compareToggle');
+        
+        if (this.comparisonMode) {
+          compareBtn.style.background = 'var(--success-color)';
+          compareBtn.title = 'Exit Compare Mode (Ctrl+C)';
+          this.showComparisonOverlay();
+        } else {
+          compareBtn.style.background = 'var(--button-bg)';
+          compareBtn.title = 'Compare Plots (Ctrl+C)';
+          this.hideComparisonOverlay();
+        }
+      }
+
+      /**
+       * Show comparison overlay
+       */
+      showComparisonOverlay() {
+        const overlay = document.getElementById('comparisonOverlay');
+        overlay.classList.add('open');
+      }
+
+      /**
+       * Hide comparison overlay
+       */
+      hideComparisonOverlay() {
+        const overlay = document.getElementById('comparisonOverlay');
+        overlay.classList.remove('open');
+        this.comparisonMode = false;
+        
+        const compareBtn = document.getElementById('compareToggle');
+        compareBtn.style.background = 'var(--button-bg)';
+        compareBtn.title = 'Compare Plots (Ctrl+C)';
+      }
+
+      /**
+       * Close comparison overlay (alias for hideComparisonOverlay)
+       */
+      closeComparison() {
+        this.hideComparisonOverlay();
+      }
+
+      /**
+       * Select plot for comparison - simple approach
+       */
+      selectPlotForComparison(slot) {
+        this.comparisonSlot = slot;
+        
+        // Hide overlay temporarily
+        const overlay = document.getElementById('comparisonOverlay');
+        overlay.style.display = 'none';
+        
+        // Show simple alert with instructions
+        const instruction = document.createElement('div');
+        instruction.id = 'comparisonInstruction';
+        instruction.style.cssText = `
+          position: fixed;
+          top: 20px;
+          left: 50%;
+          transform: translateX(-50%);
+          background: var(--button-bg);
+          color: white;
+          padding: 1rem 2rem;
+          border-radius: 8px;
+          z-index: 3000;
+          font-size: 1.1rem;
+          font-weight: 600;
+          box-shadow: 0 4px 20px rgba(0,0,0,0.3);
+        `;
+        instruction.innerHTML = `📊 Click any plot to select for ${slot === 'left' ? 'Plot A' : 'Plot B'} (ESC to cancel)`;
+        document.body.appendChild(instruction);
+        
+        // Add one-time click listener to all grid items
+        const gridItems = document.querySelectorAll('.grid-item');
+        const handleClick = (event) => {
+          event.preventDefault();
+          event.stopPropagation();
+          
+          const gridItem = event.currentTarget;
+          const img = gridItem.querySelector('img');
+          const nameEl = gridItem.querySelector('.plot-name');
+          
+          if (img && nameEl) {
+            const plotInfo = {
+              name: nameEl.textContent.trim(),
+              imgSrc: img.src,
+              pdfSrc: img.src.replace('.png', '.pdf'),
+              path: window.location.pathname
+            };
+            
+            this.addPlotToComparison(plotInfo, slot);
+          }
+          
+          // Clean up
+          instruction.remove();
+          gridItems.forEach(item => item.removeEventListener('click', handleClick));
+          overlay.style.display = 'flex';
+        };
+        
+        gridItems.forEach(item => {
+          item.style.cursor = 'pointer';
+          item.style.border = '2px dashed var(--button-bg)';
+          item.addEventListener('click', handleClick);
+        });
+        
+        // ESC to cancel
+        const handleEscape = (event) => {
+          if (event.key === 'Escape') {
+            instruction.remove();
+            gridItems.forEach(item => {
+              item.removeEventListener('click', handleClick);
+              item.style.cursor = '';
+              item.style.border = '';
+            });
+            overlay.style.display = 'flex';
+            document.removeEventListener('keydown', handleEscape);
+          }
+        };
+        document.addEventListener('keydown', handleEscape);
+      }
+
+      /**
+       * Add plot to comparison panel
+       */
+      addPlotToComparison(plotInfo, slot) {
+        this.plots[slot] = plotInfo;
+        
+        const container = document.getElementById(`${slot}PlotContainer`);
+        const title = document.getElementById(`${slot}PlotTitle`);
+        const replaceBtn = document.getElementById(`${slot}ReplaceBtn`);
+        
+        container.innerHTML = `
+          <img src="${plotInfo.imgSrc}" class="comparison-plot" alt="${plotInfo.name}" 
+               onclick="window.open('${plotInfo.pdfSrc}', '_blank')" />
+          <div class="comparison-plot-info">
+            <strong>${plotInfo.name}</strong><br>
+            <small>${plotInfo.path}</small>
+          </div>
+        `;
+        
+        title.textContent = plotInfo.name;
+        replaceBtn.style.display = 'block';
+        
+        // Reset grid item styles
+        const gridItems = document.querySelectorAll('.grid-item');
+        gridItems.forEach(item => {
+          item.style.cursor = '';
+          item.style.border = '';
+        });
+      }
+
+      /**
+       * Replace plot in comparison
+       */
+      replacePlot(slot) {
+        this.selectPlotForComparison(slot);
+      }
     }
 
     // ========================================