diff --git a/web/src/app/chat/Refinement.tsx b/web/src/app/chat/Refinement.tsx
index fe679ed9a..df296eb8d 100644
--- a/web/src/app/chat/Refinement.tsx
+++ b/web/src/app/chat/Refinement.tsx
@@ -28,11 +28,7 @@ export function useOrderedPhases(externalPhase: StreamingPhase) {
   // Whenever externalPhase changes, add any missing steps into the queue
   useEffect(() => {
     setPhaseQueue((prevQueue) => {
-      const lastDisplayed = displayedPhases[displayedPhases.length - 1];
       const lastIndex = finalPhaseIndex.current || 0;
-      //  lastDisplayed
-      //   ? getPhaseIndex(lastDisplayed)
-      //   : getPhaseIndex(StreamingPhase.WAITING);
 
       let targetPhase = externalPhase;
       let targetIndex = getPhaseIndex(targetPhase);
@@ -50,11 +46,6 @@ export function useOrderedPhases(externalPhase: StreamingPhase) {
         targetIndex + 1
       );
 
-      // [];
-
-      // for (let i = lastIndex + 1; i <= targetIndex; i++) {
-      //   missingPhases= PHASES_ORDER[i]);
-      // }
       return [...prevQueue, ...missingPhases];
     });
   }, [externalPhase, displayedPhases]);
@@ -125,6 +116,7 @@ export function RefinemenetBadge({
 
   // Expand/collapse, hover states
   const [expanded, setExpanded] = useState(true);
+  const [toolTipHoveredInternal, setToolTipHoveredInternal] = useState(false);
   const [isHovered, setIsHovered] = useState(false);
   const [shouldShow, setShouldShow] = useState(true);
 
@@ -145,7 +137,7 @@ export function RefinemenetBadge({
 
   return (
     <TooltipProvider delayDuration={0}>
-      <Tooltip>
+      <Tooltip open={isHovered || toolTipHoveredInternal}>
         <div
           className="relative w-fit max-w-sm"
           onMouseEnter={() => setIsHovered(true)}
@@ -167,10 +159,16 @@ export function RefinemenetBadge({
           </TooltipTrigger>
           {expanded && (
             <TooltipContent
-              onMouseEnter={() => setToolTipHovered(true)}
+              onMouseEnter={() => {
+                setToolTipHoveredInternal(true);
+                setToolTipHovered(true);
+              }}
+              onMouseLeave={() => {
+                setToolTipHoveredInternal(false);
+              }}
               side="bottom"
               align="start"
-              className="w-fit p-4 bg-white border-2 border-border shadow-lg rounded-md"
+              className="w-fit  -mt-1 p-4 bg-white border-2 border-border shadow-lg rounded-md"
             >
               {/* If not done, show the "Refining" box + a chevron */}
 
@@ -322,7 +320,9 @@ export function StatusRefinement({
                 <Badge
                   // NOTE: This is a hack to make the badge slightly higher
                   className="cursor-pointer mt-[1px]"
-                  variant="agent"
+                  variant={`${
+                    isViewingInitialAnswer ? "agent" : "agent-faded"
+                  }`}
                   onClick={() => {
                     const viewInitialAnswer = !isViewingInitialAnswer;
                     setIsViewingInitialAnswer(viewInitialAnswer);
diff --git a/web/src/app/chat/message/AgenticMessage.tsx b/web/src/app/chat/message/AgenticMessage.tsx
index 867485008..3b9843a46 100644
--- a/web/src/app/chat/message/AgenticMessage.tsx
+++ b/web/src/app/chat/message/AgenticMessage.tsx
@@ -147,7 +147,7 @@ export const AgenticMessage = ({
 
     processed = processed.replace(/\]\](?!\()/g, "]]()");
 
-    return preprocessLaTeX(processed) + (!isComplete ? " [*]() " : "");
+    return preprocessLaTeX(processed);
   };
 
   const finalContent = processContent(content) as string;
@@ -322,10 +322,11 @@ export const AgenticMessage = ({
         remarkPlugins={[remarkGfm, remarkMath]}
         rehypePlugins={[[rehypePrism, { ignoreMissing: true }], rehypeKatex]}
       >
-        {streamedContent}
+        {streamedContent +
+          (!isComplete && !secondLevelGenerating ? " [*]() " : "")}
       </ReactMarkdown>
     );
-  }, [streamedContent, markdownComponents]);
+  }, [streamedContent, markdownComponents, isComplete]);
 
   const includeMessageSwitcher =
     currentMessageInd !== undefined &&
@@ -335,10 +336,6 @@ export const AgenticMessage = ({
 
   useEffect(() => {
     if (!allowStreaming) {
-      //   if (typeof content === "string") {
-      //     setStreamedContent(finalContent);
-      //     setLastKnownContentLength(finalContent.length);
-      //   }
       return;
     }
 
diff --git a/web/src/app/chat/message/MemoizedTextComponents.tsx b/web/src/app/chat/message/MemoizedTextComponents.tsx
index fbb67dadd..9fbfd4bd2 100644
--- a/web/src/app/chat/message/MemoizedTextComponents.tsx
+++ b/web/src/app/chat/message/MemoizedTextComponents.tsx
@@ -31,7 +31,7 @@ export const MemoizedAnchor = memo(
     if (value?.startsWith("[") && value?.endsWith("]")) {
       const match = value.match(/\[(D|Q)?(\d+)\]/);
       if (match) {
-        const index = parseInt(match[1], 10) - 1;
+        const index = parseInt(match[2], 10) - 1;
         const associatedDoc = docs?.[index];
         if (!associatedDoc) {
           return <a href={children as string}>{children}</a>;
@@ -53,7 +53,7 @@ export const MemoizedAnchor = memo(
         if (!associatedDoc && !associatedSubQuestion) {
           return (
             <>
-              {children}
+              l{children}
               {/* No associated docs or subquestions.
               <div className="text-sm text-gray-600">
                 <p>Number of questions: {subQuestions?.length}</p>
@@ -114,7 +114,7 @@ export const MemoizedAnchor = memo(
     }
     return (
       <MemoizedLink updatePresentingDocument={updatePresentingDocument}>
-        {children}
+        {children}l
       </MemoizedLink>
     );
   }
diff --git a/web/src/components/ui/badge.tsx b/web/src/components/ui/badge.tsx
index 387d457e1..3b2746600 100644
--- a/web/src/components/ui/badge.tsx
+++ b/web/src/components/ui/badge.tsx
@@ -8,6 +8,8 @@ const badgeVariants = cva(
   {
     variants: {
       variant: {
+        "agent-faded":
+          "border-neutral-200 bg-neutral-100 text-neutral-600 hover:bg-neutral-200",
         agent: "border-agent bg-agent text-white hover:bg-agent-hover",
         canceled:
           "border-gray-200 bg-gray-50 text-gray-600 hover:bg-gray-75 dark:bg-gray-900 dark:text-neutral-50 dark:hover:bg-gray-850",