diff --git a/doc/source/development/index.rst b/doc/source/development/index.rst
index d67a6c3a2ca04..a149f31118ed5 100644
--- a/doc/source/development/index.rst
+++ b/doc/source/development/index.rst
@@ -6,6 +6,9 @@
 Development
 ===========
 
+.. If you update this toctree, also update the manual toctree in the
+   main index.rst.template
+
 .. toctree::
     :maxdepth: 2
 
diff --git a/doc/source/getting_started/index.rst b/doc/source/getting_started/index.rst
index 4c5d26461a667..eead28830f861 100644
--- a/doc/source/getting_started/index.rst
+++ b/doc/source/getting_started/index.rst
@@ -6,6 +6,9 @@
 Getting started
 ===============
 
+.. If you update this toctree, also update the manual toctree in the
+   main index.rst.template
+
 .. toctree::
     :maxdepth: 2
 
diff --git a/doc/source/index.rst.template b/doc/source/index.rst.template
index df2a29a76f3c5..0f82592f084f4 100644
--- a/doc/source/index.rst.template
+++ b/doc/source/index.rst.template
@@ -25,7 +25,7 @@ See the :ref:`overview` for more detail about what's in the library.
 
 {% if single_doc and single_doc.endswith('.rst') -%}
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 3
 
     {{ single_doc[:-4] }}
 {% elif single_doc %}
@@ -35,7 +35,8 @@ See the :ref:`overview` for more detail about what's in the library.
     {{ single_doc }}
 {% else -%}
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 3
+    :hidden:
 {% endif %}
 
     {% if not single_doc -%}
@@ -51,4 +52,67 @@ See the :ref:`overview` for more detail about what's in the library.
     {% if not single_doc -%}
     development/index
     whatsnew/index
-    {% endif -%}
+{% endif -%}
+
+
+* :doc:`whatsnew/v0.25.0`
+* :doc:`install`
+* :doc:`getting_started/index`
+
+  * :doc:`getting_started/overview`
+  * :doc:`getting_started/10min`
+  * :doc:`getting_started/basics`
+  * :doc:`getting_started/dsintro`
+  * :doc:`getting_started/comparison/index`
+  * :doc:`getting_started/tutorials`
+
+* :doc:`user_guide/index`
+
+  * :doc:`user_guide/io`
+  * :doc:`user_guide/indexing`
+  * :doc:`user_guide/advanced`
+  * :doc:`user_guide/merging`
+  * :doc:`user_guide/reshaping`
+  * :doc:`user_guide/text`
+  * :doc:`user_guide/missing_data`
+  * :doc:`user_guide/categorical`
+  * :doc:`user_guide/integer_na`
+  * :doc:`user_guide/visualization`
+  * :doc:`user_guide/computation`
+  * :doc:`user_guide/groupby`
+  * :doc:`user_guide/timeseries`
+  * :doc:`user_guide/timedeltas`
+  * :doc:`user_guide/style`
+  * :doc:`user_guide/options`
+  * :doc:`user_guide/enhancingperf`
+  * :doc:`user_guide/sparse`
+  * :doc:`user_guide/gotchas`
+  * :doc:`user_guide/cookbook`
+
+* :doc:`ecosystem`
+* :doc:`reference/index`
+
+  * :doc:`reference/io`
+  * :doc:`reference/general_functions`
+  * :doc:`reference/series`
+  * :doc:`reference/frame`
+  * :doc:`reference/arrays`
+  * :doc:`reference/panel`
+  * :doc:`reference/indexing`
+  * :doc:`reference/offset_frequency`
+  * :doc:`reference/window`
+  * :doc:`reference/groupby`
+  * :doc:`reference/resampling`
+  * :doc:`reference/style`
+  * :doc:`reference/plotting`
+  * :doc:`reference/general_utility_functions`
+  * :doc:`reference/extensions`
+
+* :doc:`development/index`
+
+  * :doc:`development/contributing`
+  * :doc:`development/internals`
+  * :doc:`development/extending`
+  * :doc:`development/developer`
+
+* :doc:`whatsnew/index`
diff --git a/doc/source/reference/index.rst b/doc/source/reference/index.rst
index ef4676054473a..1e652c9e5497d 100644
--- a/doc/source/reference/index.rst
+++ b/doc/source/reference/index.rst
@@ -19,6 +19,9 @@ public functions related to data types in pandas.
 
     The ``pandas.core``, ``pandas.compat``, and ``pandas.util`` top-level modules are PRIVATE. Stable functionality in such modules is not guaranteed.
 
+.. If you update this toctree, also update the manual toctree in the
+   main index.rst.template
+
 .. toctree::
    :maxdepth: 2
 
@@ -41,40 +44,40 @@ public functions related to data types in pandas.
 .. This is to prevent warnings in the doc build. We don't want to encourage
 .. these methods.
 
-.. toctree::
-   :hidden:
-
-   api/pandas.DataFrame.blocks
-   api/pandas.DataFrame.as_matrix
-   api/pandas.DataFrame.ix
-   api/pandas.Index.asi8
-   api/pandas.Index.data
-   api/pandas.Index.flags
-   api/pandas.Index.holds_integer
-   api/pandas.Index.is_type_compatible
-   api/pandas.Index.nlevels
-   api/pandas.Index.sort
-   api/pandas.Panel.agg
-   api/pandas.Panel.aggregate
-   api/pandas.Panel.blocks
-   api/pandas.Panel.empty
-   api/pandas.Panel.is_copy
-   api/pandas.Panel.items
-   api/pandas.Panel.ix
-   api/pandas.Panel.major_axis
-   api/pandas.Panel.minor_axis
-   api/pandas.Series.asobject
-   api/pandas.Series.blocks
-   api/pandas.Series.from_array
-   api/pandas.Series.ix
-   api/pandas.Series.imag
-   api/pandas.Series.real
+..
+    .. toctree::
+
+        api/pandas.DataFrame.blocks
+        api/pandas.DataFrame.as_matrix
+        api/pandas.DataFrame.ix
+        api/pandas.Index.asi8
+        api/pandas.Index.data
+        api/pandas.Index.flags
+        api/pandas.Index.holds_integer
+        api/pandas.Index.is_type_compatible
+        api/pandas.Index.nlevels
+        api/pandas.Index.sort
+        api/pandas.Panel.agg
+        api/pandas.Panel.aggregate
+        api/pandas.Panel.blocks
+        api/pandas.Panel.empty
+        api/pandas.Panel.is_copy
+        api/pandas.Panel.items
+        api/pandas.Panel.ix
+        api/pandas.Panel.major_axis
+        api/pandas.Panel.minor_axis
+        api/pandas.Series.asobject
+        api/pandas.Series.blocks
+        api/pandas.Series.from_array
+        api/pandas.Series.ix
+        api/pandas.Series.imag
+        api/pandas.Series.real
 
 
 .. Can't convince sphinx to generate toctree for this class attribute.
 .. So we do it manually to avoid a warning
 
-.. toctree::
-   :hidden:
+..
+    .. toctree::
 
-   api/pandas.api.extensions.ExtensionDtype.na_value
+        api/pandas.api.extensions.ExtensionDtype.na_value
diff --git a/doc/source/themes/nature_with_gtoc/layout.html b/doc/source/themes/nature_with_gtoc/layout.html
index a2106605c5562..b3f13f99f44d4 100644
--- a/doc/source/themes/nature_with_gtoc/layout.html
+++ b/doc/source/themes/nature_with_gtoc/layout.html
@@ -19,7 +19,7 @@
                 {%- block sidebar1 %}
                 {%- block sidebartoc %}
                 <h3>{{ _('Table Of Contents') }}</h3>
-                {{ toctree() }}
+                {{ toctree(includehidden=True) }}
                 {%- endblock %}
                 {%- block sidebarsearch %}
                 <h3 style="margin-top: 1.5em;">{{ _('Search') }}</h3>
@@ -105,4 +105,4 @@ <h3 style="margin-top: 1.5em;">{{ _('Search') }}</h3>
     var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
   })();
 </script>
-{% endblock %}
\ No newline at end of file
+{% endblock %}
diff --git a/doc/source/user_guide/index.rst b/doc/source/user_guide/index.rst
index d39cf7103ab63..05df83decbd7e 100644
--- a/doc/source/user_guide/index.rst
+++ b/doc/source/user_guide/index.rst
@@ -15,6 +15,9 @@ Users brand-new to pandas should start with :ref:`10min`.
 Further information on any specific method can be obtained in the
 :ref:`api`.
 
+.. If you update this toctree, also update the manual toctree in the
+   main index.rst.template
+
 .. toctree::
     :maxdepth: 2