diff --git a/src/core/processing-queue.js b/src/core/processing-queue.js
index 324df180f..ab7323370 100644
--- a/src/core/processing-queue.js
+++ b/src/core/processing-queue.js
@@ -194,9 +194,6 @@ class ProcessingQueue {
     const runEnd = runSuite.end(true);
     emit('runEnd', runEnd);
 
-    const runtime = runEnd.runtime;
-    const passed = config.stats.all - config.stats.bad;
-
     runLoggingCallbacks('done', {
       // Use of "details" parameter to QUnit.done() is discouraged
       // since QUnit 2.19 to solve the "assertion counting" gotchas
@@ -204,17 +201,22 @@ class ProcessingQueue {
       // Use QUnit.on('runEnd') instead.
       //
       // Kept for compatibility with ecosystem integrations
-      // such as Testem, which safely only the "runtime" field only.
-      passed,
+      // such as Testem, which safely use the "runtime" field only.
+      passed: config.stats.all - config.stats.bad,
       failed: config.stats.bad,
       total: config.stats.all,
-      runtime
+      runtime: runEnd.runtime
     }).then(() => {
-      // Clear own storage items if all tests passed
-      if (storage && config.stats.bad === 0) {
+      // Clear our storage keys if run passed and there were no "todo" tests left.
+      //
+      // The check for "todo" is important, because after a passing run,
+      // it is useful for re-runs to quickly start with known "todo" tests.
+      // In test.js we inform storage about "todo" failures the same as
+      // any other failure. Clearing here after merely "passed" would defeat
+      // that logic.
+      if (storage && runEnd.status === 'passed' && !runEnd.testCounts.todo) {
         for (let i = storage.length - 1; i >= 0; i--) {
           const key = storage.key(i);
-
           if (key.indexOf('qunit-test-') === 0) {
             storage.removeItem(key);
           }
diff --git a/src/test.js b/src/test.js
index b03d5f138..31fcf9f5b 100644
--- a/src/test.js
+++ b/src/test.js
@@ -379,12 +379,10 @@ Test.prototype = {
     module.stats.all += this.assertions.length;
 
     for (let i = 0; i < this.assertions.length; i++) {
-      // A failing assertion will counts toward the HTML Reporter's
-      // "X assertions, Y failed" line even if it was inside a todo.
-      // Inverting this would be similarly confusing since all but the last
-      // passing assertion inside a todo test should be considered as good.
-      // These stats don't decide the outcome of anything, so counting them
-      // as failing seems the most intuitive.
+      // For legacy reasons, `config.stats` reflects raw assertion counts.
+      // This means all failures add to the "bad" count, even an expected
+      // failure inside a passing "todo" test.
+      // See also https://qunitjs.com/api/callbacks/QUnit.done/
       if (!this.assertions[i].result) {
         bad++;
         config.stats.bad++;