diff --git a/src/Elastic.ApiExplorer/OpenApiGenerator.cs b/src/Elastic.ApiExplorer/OpenApiGenerator.cs
index cb08b4cde..ec68fc819 100644
--- a/src/Elastic.ApiExplorer/OpenApiGenerator.cs
+++ b/src/Elastic.ApiExplorer/OpenApiGenerator.cs
@@ -288,7 +288,7 @@ private async Task<IFileInfo> Render<T>(INavigationItem current, T page, ApiRend
 		if (!outputFile.Directory!.Exists)
 			outputFile.Directory.Create();
 
-		var navigationRenderResult = await navigationRenderer.RenderNavigation(current.NavigationRoot, new Uri("http://ignored.example"), INavigationHtmlWriter.AllLevels, ctx);
+		var navigationRenderResult = await navigationRenderer.RenderNavigation(current.NavigationRoot, INavigationHtmlWriter.AllLevels, ctx);
 		renderContext = renderContext with
 		{
 			CurrentNavigation = current,
diff --git a/src/Elastic.Documentation.Site/Navigation/INavigationHtmlWriter.cs b/src/Elastic.Documentation.Site/Navigation/INavigationHtmlWriter.cs
index cf86b765c..3f598bcac 100644
--- a/src/Elastic.Documentation.Site/Navigation/INavigationHtmlWriter.cs
+++ b/src/Elastic.Documentation.Site/Navigation/INavigationHtmlWriter.cs
@@ -10,8 +10,7 @@ public interface INavigationHtmlWriter
 {
 	const int AllLevels = -1;
 
-	Task<NavigationRenderResult> RenderNavigation(IRootNavigationItem<INavigationModel, INavigationItem> currentRootNavigation, Uri navigationSource,
-		int maxLevel, Cancel ctx = default);
+	Task<NavigationRenderResult> RenderNavigation(IRootNavigationItem<INavigationModel, INavigationItem> currentRootNavigation, int maxLevel, Cancel ctx = default);
 
 	async Task<string> Render(NavigationViewModel model, Cancel ctx)
 	{
diff --git a/src/Elastic.Documentation.Site/Navigation/IsolatedBuildNavigationHtmlWriter.cs b/src/Elastic.Documentation.Site/Navigation/IsolatedBuildNavigationHtmlWriter.cs
index e0c3c5d29..198405d18 100644
--- a/src/Elastic.Documentation.Site/Navigation/IsolatedBuildNavigationHtmlWriter.cs
+++ b/src/Elastic.Documentation.Site/Navigation/IsolatedBuildNavigationHtmlWriter.cs
@@ -13,8 +13,9 @@ public class IsolatedBuildNavigationHtmlWriter(BuildContext context, IRootNaviga
 {
 	private readonly ConcurrentDictionary<(string, int), string> _renderedNavigationCache = [];
 
-	public async Task<NavigationRenderResult> RenderNavigation(IRootNavigationItem<INavigationModel, INavigationItem> currentRootNavigation,
-		Uri navigationSource, int maxLevel, Cancel ctx = default)
+	public async Task<NavigationRenderResult> RenderNavigation(
+		IRootNavigationItem<INavigationModel, INavigationItem> currentRootNavigation, int maxLevel, Cancel ctx = default
+	)
 	{
 		var navigation = context.Configuration.Features.PrimaryNavEnabled || currentRootNavigation.IsUsingNavigationDropdown
 			? currentRootNavigation
diff --git a/src/Elastic.Markdown/HtmlWriter.cs b/src/Elastic.Markdown/HtmlWriter.cs
index b53e57a5a..7a21f0481 100644
--- a/src/Elastic.Markdown/HtmlWriter.cs
+++ b/src/Elastic.Markdown/HtmlWriter.cs
@@ -56,8 +56,8 @@ private async Task<RenderResult> RenderLayout(MarkdownFile markdown, MarkdownDoc
 		var html = MarkdownFile.CreateHtml(document);
 		await DocumentationSet.Tree.Resolve(ctx);
 
-		var fullNavigationRenderResult = await NavigationHtmlWriter.RenderNavigation(markdown.NavigationRoot, markdown.NavigationSource, INavigationHtmlWriter.AllLevels, ctx);
-		var miniNavigationRenderResult = await NavigationHtmlWriter.RenderNavigation(markdown.NavigationRoot, markdown.NavigationSource, 1, ctx);
+		var fullNavigationRenderResult = await NavigationHtmlWriter.RenderNavigation(markdown.NavigationRoot, INavigationHtmlWriter.AllLevels, ctx);
+		var miniNavigationRenderResult = await NavigationHtmlWriter.RenderNavigation(markdown.NavigationRoot, 1, ctx);
 
 		var navigationHtmlRenderResult = DocumentationSet.Context.Configuration.Features.LazyLoadNavigation
 			? miniNavigationRenderResult
diff --git a/src/Elastic.Markdown/IO/MarkdownFile.cs b/src/Elastic.Markdown/IO/MarkdownFile.cs
index 592d69832..6e1c21eec 100644
--- a/src/Elastic.Markdown/IO/MarkdownFile.cs
+++ b/src/Elastic.Markdown/IO/MarkdownFile.cs
@@ -57,7 +57,6 @@ DocumentationSet set
 		ScopeDirectory = build.Configuration.ScopeDirectory;
 
 		NavigationRoot = set.Tree;
-		NavigationSource = set.Source;
 	}
 
 	public bool PartOfNavigation { get; set; }
@@ -66,8 +65,6 @@ DocumentationSet set
 
 	public IRootNavigationItem<INavigationModel, INavigationItem> NavigationRoot { get; set; }
 
-	public Uri NavigationSource { get; set; }
-
 	private IDiagnosticsCollector Collector { get; }
 
 	public string? UrlPathPrefix { get; }
diff --git a/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs b/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
index 31009a135..fd7554c85 100644
--- a/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
+++ b/src/Elastic.Markdown/IO/Navigation/DocumentationGroup.cs
@@ -11,7 +11,7 @@
 
 namespace Elastic.Markdown.IO.Navigation;
 
-[DebuggerDisplay("Group >{Depth} {FolderName} ({NavigationItems.Count} items)")]
+[DebuggerDisplay("Toc: {Depth} {NavigationSource} > ({NavigationItems.Count} items)")]
 public class DocumentationGroup : INodeNavigationItem<MarkdownFile, INavigationItem>
 {
 	private readonly TableOfContentsTreeCollector _treeCollector;
@@ -138,7 +138,6 @@ void AddToNavigationItems(INavigationItem item, ref int fileIndex)
 				// TODO these have to be refactor to be pure navigational properties
 				md.ScopeDirectory = file.TableOfContentsScope.ScopeDirectory;
 				md.NavigationRoot = rootNavigationItem;
-				md.NavigationSource = NavigationSource;
 
 				foreach (var extension in lookups.EnabledExtensions)
 					extension.Visit(d, tocItem);
diff --git a/src/Elastic.Markdown/IO/Navigation/TableOfContentsTree.cs b/src/Elastic.Markdown/IO/Navigation/TableOfContentsTree.cs
index f2e92e695..d9caeb648 100644
--- a/src/Elastic.Markdown/IO/Navigation/TableOfContentsTree.cs
+++ b/src/Elastic.Markdown/IO/Navigation/TableOfContentsTree.cs
@@ -8,7 +8,7 @@
 
 namespace Elastic.Markdown.IO.Navigation;
 
-[DebuggerDisplay("Toc >{Depth} {FolderName} ({NavigationItems.Count} items)")]
+[DebuggerDisplay("Toc: {Depth} {NavigationSource} > ({NavigationItems.Count} items)")]
 public class TableOfContentsTree : DocumentationGroup, IRootNavigationItem<MarkdownFile, INavigationItem>
 {
 	public Uri Source { get; }
diff --git a/src/Elastic.Markdown/IO/Navigation/TableOfContentsTreeCollector.cs b/src/Elastic.Markdown/IO/Navigation/TableOfContentsTreeCollector.cs
index 47d8e8547..103a91a93 100644
--- a/src/Elastic.Markdown/IO/Navigation/TableOfContentsTreeCollector.cs
+++ b/src/Elastic.Markdown/IO/Navigation/TableOfContentsTreeCollector.cs
@@ -11,11 +11,7 @@ public class TableOfContentsTreeCollector
 {
 	private Dictionary<Uri, TableOfContentsTree> NestedTableOfContentsTrees { get; } = [];
 
-	public void Collect(Uri source, TableOfContentsTree tree) =>
-		NestedTableOfContentsTrees[source] = tree;
-
-	public void Collect(TocReference tocReference, TableOfContentsTree tree) =>
-		NestedTableOfContentsTrees[tocReference.Source] = tree;
+	public void Collect(Uri source, TableOfContentsTree tree) => NestedTableOfContentsTrees[source] = tree;
 
 	public bool TryGetTableOfContentsTree(Uri source, [NotNullWhen(true)] out TableOfContentsTree? tree) =>
 		NestedTableOfContentsTrees.TryGetValue(source, out tree);
diff --git a/src/tooling/docs-assembler/AssembleSources.cs b/src/tooling/docs-assembler/AssembleSources.cs
index 1bdcf6396..9ffe0664d 100644
--- a/src/tooling/docs-assembler/AssembleSources.cs
+++ b/src/tooling/docs-assembler/AssembleSources.cs
@@ -20,7 +20,8 @@
 using YamlDotNet.RepresentationModel;
 
 namespace Documentation.Assembler;
-public record TocTopLevelMapping
+
+public record NavigationTocMapping
 {
 	public required Uri Source { get; init; }
 	public required string SourcePathPrefix { get; init; }
@@ -30,7 +31,7 @@ public record TocTopLevelMapping
 
 public record TocConfigurationMapping
 {
-	public required TocTopLevelMapping TopLevel { get; init; }
+	public required NavigationTocMapping TopLevel { get; init; }
 	public required ConfigurationFile RepositoryConfigurationFile { get; init; }
 	public required TableOfContentsConfiguration TableOfContentsConfiguration { get; init; }
 }
@@ -40,7 +41,7 @@ public class AssembleSources
 	public AssembleContext AssembleContext { get; }
 	public FrozenDictionary<string, AssemblerDocumentationSet> AssembleSets { get; }
 
-	public FrozenDictionary<Uri, TocTopLevelMapping> TocTopLevelMappings { get; }
+	public FrozenDictionary<Uri, NavigationTocMapping> NavigationTocMappings { get; }
 
 	public FrozenDictionary<string, IReadOnlyCollection<string>> HistoryMappings { get; }
 
@@ -61,11 +62,11 @@ public static async Task<AssembleSources> AssembleAsync(ILoggerFactory logger, A
 	private AssembleSources(ILoggerFactory logger, AssembleContext assembleContext, Checkout[] checkouts, VersionsConfiguration versionsConfiguration)
 	{
 		AssembleContext = assembleContext;
-		TocTopLevelMappings = GetConfiguredSources(assembleContext);
+		NavigationTocMappings = GetTocMappings(assembleContext);
 		HistoryMappings = GetHistoryMapping(assembleContext);
 		var linkIndexProvider = Aws3LinkIndexReader.CreateAnonymous();
 		var crossLinkFetcher = new AssemblerCrossLinkFetcher(logger, assembleContext.Configuration, assembleContext.Environment, linkIndexProvider);
-		UriResolver = new PublishEnvironmentUriResolver(TocTopLevelMappings, assembleContext.Environment);
+		UriResolver = new PublishEnvironmentUriResolver(NavigationTocMappings, assembleContext.Environment);
 		var crossLinkResolver = new CrossLinkResolver(crossLinkFetcher, UriResolver);
 		AssembleSets = checkouts
 			.Where(c => c.Repository is { Skip: false })
@@ -73,7 +74,7 @@ private AssembleSources(ILoggerFactory logger, AssembleContext assembleContext,
 			.ToDictionary(s => s.Checkout.Repository.Name, s => s)
 			.ToFrozenDictionary();
 
-		TocConfigurationMapping = TocTopLevelMappings
+		TocConfigurationMapping = NavigationTocMappings
 			.Select(kv =>
 			{
 				var repo = kv.Value.Source.Scheme;
@@ -148,11 +149,11 @@ static void ReadHistoryMappings(IDictionary<string, IReadOnlyCollection<string>>
 	}
 
 
-	public static FrozenDictionary<Uri, TocTopLevelMapping> GetConfiguredSources(AssembleContext context)
+	public static FrozenDictionary<Uri, NavigationTocMapping> GetTocMappings(AssembleContext context)
 	{
-		var dictionary = new Dictionary<Uri, TocTopLevelMapping>();
+		var dictionary = new Dictionary<Uri, NavigationTocMapping>();
 		var reader = new YamlStreamReader(context.NavigationPath, context.Collector);
-		var entries = new List<KeyValuePair<Uri, TocTopLevelMapping>>();
+		var entries = new List<KeyValuePair<Uri, NavigationTocMapping>>();
 		foreach (var entry in reader.Read())
 		{
 			switch (entry.Key)
@@ -167,7 +168,7 @@ public static FrozenDictionary<Uri, TocTopLevelMapping> GetConfiguredSources(Ass
 		return dictionary.ToFrozenDictionary();
 
 		static void ReadTocBlocks(
-			List<KeyValuePair<Uri, TocTopLevelMapping>> entries,
+			List<KeyValuePair<Uri, NavigationTocMapping>> entries,
 			YamlStreamReader reader,
 			KeyValuePair<YamlNode, YamlNode> entry,
 			string? parent,
@@ -196,7 +197,7 @@ static void ReadTocBlocks(
 			}
 		}
 		static void ReadBlock(
-			List<KeyValuePair<Uri, TocTopLevelMapping>> entries,
+			List<KeyValuePair<Uri, NavigationTocMapping>> entries,
 			YamlStreamReader reader,
 			YamlMappingNode tocEntry,
 			string? parent,
@@ -259,14 +260,14 @@ static void ReadBlock(
 			topLevelSource ??= sourceUri;
 			parentSource ??= sourceUri;
 
-			var tocTopLevelMapping = new TocTopLevelMapping
+			var tocTopLevelMapping = new NavigationTocMapping
 			{
 				Source = sourceUri,
 				SourcePathPrefix = pathPrefix,
 				TopLevelSource = topLevelSource,
 				ParentSource = parentSource
 			};
-			entries.Add(new KeyValuePair<Uri, TocTopLevelMapping>(sourceUri, tocTopLevelMapping));
+			entries.Add(new KeyValuePair<Uri, NavigationTocMapping>(sourceUri, tocTopLevelMapping));
 
 			foreach (var entry in tocEntry.Children)
 			{
diff --git a/src/tooling/docs-assembler/Building/PublishEnvironmentUriResolver.cs b/src/tooling/docs-assembler/Building/PublishEnvironmentUriResolver.cs
index ad2ee16c3..528e3480a 100644
--- a/src/tooling/docs-assembler/Building/PublishEnvironmentUriResolver.cs
+++ b/src/tooling/docs-assembler/Building/PublishEnvironmentUriResolver.cs
@@ -11,14 +11,14 @@ namespace Documentation.Assembler.Building;
 
 public class PublishEnvironmentUriResolver : IUriEnvironmentResolver
 {
-	private readonly FrozenDictionary<Uri, TocTopLevelMapping> _topLevelMappings;
+	private readonly FrozenDictionary<Uri, NavigationTocMapping> _topLevelMappings;
 	private Uri BaseUri { get; }
 
 	private PublishEnvironment PublishEnvironment { get; }
 
 	private IReadOnlyList<string> TableOfContentsPrefixes { get; }
 
-	public PublishEnvironmentUriResolver(FrozenDictionary<Uri, TocTopLevelMapping> topLevelMappings, PublishEnvironment environment)
+	public PublishEnvironmentUriResolver(FrozenDictionary<Uri, NavigationTocMapping> topLevelMappings, PublishEnvironment environment)
 	{
 		_topLevelMappings = topLevelMappings;
 		PublishEnvironment = environment;
diff --git a/src/tooling/docs-assembler/Cli/RepositoryCommands.cs b/src/tooling/docs-assembler/Cli/RepositoryCommands.cs
index b2b514cb9..a94e734d2 100644
--- a/src/tooling/docs-assembler/Cli/RepositoryCommands.cs
+++ b/src/tooling/docs-assembler/Cli/RepositoryCommands.cs
@@ -130,7 +130,7 @@ public async Task<int> BuildAll(
 		var navigation = new GlobalNavigation(assembleSources, navigationFile);
 
 		var pathProvider = new GlobalNavigationPathProvider(navigationFile, assembleSources, assembleContext);
-		var htmlWriter = new GlobalNavigationHtmlWriter(navigationFile, assembleContext, navigation, assembleSources);
+		var htmlWriter = new GlobalNavigationHtmlWriter(logger, navigation);
 		var legacyPageChecker = new LegacyPageChecker();
 		var historyMapper = new PageLegacyUrlMapper(legacyPageChecker, assembleSources.HistoryMappings);
 
diff --git a/src/tooling/docs-assembler/Links/NavigationPrefixChecker.cs b/src/tooling/docs-assembler/Links/NavigationPrefixChecker.cs
index 399b6c0b1..f66128d0f 100644
--- a/src/tooling/docs-assembler/Links/NavigationPrefixChecker.cs
+++ b/src/tooling/docs-assembler/Links/NavigationPrefixChecker.cs
@@ -53,7 +53,7 @@ public NavigationPrefixChecker(ILoggerFactory logger, AssembleContext context)
 		_logger = logger.CreateLogger<NavigationPrefixChecker>();
 		_loggerFactory = logger;
 
-		var tocTopLevelMappings = AssembleSources.GetConfiguredSources(context);
+		var tocTopLevelMappings = AssembleSources.GetTocMappings(context);
 		_uriResolver = new PublishEnvironmentUriResolver(tocTopLevelMappings, context.Environment);
 	}
 
diff --git a/src/tooling/docs-assembler/Navigation/GlobalNavigation.cs b/src/tooling/docs-assembler/Navigation/GlobalNavigation.cs
index 14b921ff0..f028616cd 100644
--- a/src/tooling/docs-assembler/Navigation/GlobalNavigation.cs
+++ b/src/tooling/docs-assembler/Navigation/GlobalNavigation.cs
@@ -3,6 +3,8 @@
 // See the LICENSE file in the project root for more information
 
 using System.Collections.Frozen;
+using System.Collections.Immutable;
+using Elastic.Documentation.Configuration.Assembler;
 using Elastic.Documentation.Configuration.TableOfContents;
 using Elastic.Documentation.Site.Navigation;
 using Elastic.Markdown.IO;
@@ -25,14 +27,28 @@ public record GlobalNavigation : IPositionalNavigation
 
 	public FrozenDictionary<int, INavigationItem> NavigationIndexedByOrder { get; }
 
+	private ImmutableHashSet<Uri> Phantoms { get; }
+
+	private TableOfContentsTree RootContentTree { get; }
+
 	public GlobalNavigation(AssembleSources assembleSources, GlobalNavigationFile navigationFile)
 	{
 		_assembleSources = assembleSources;
 		_navigationFile = navigationFile;
-		NavigationItems = BuildNavigation(navigationFile.TableOfContents.Concat(navigationFile.Phantoms).ToArray(), 0);
+
+		// the root files of `docs-content://` are special they contain several special pages such as 404, archive, versions etc.
+		// we inject them forcefully here
+		var source = new Uri($"{NarrativeRepository.RepositoryName}://");
+		RootContentTree = assembleSources.TreeCollector.TryGetTableOfContentsTree(source, out var docsContentTree)
+			? docsContentTree
+			: throw new Exception($"Could not locate: {source} as root of global navigation.");
+		Phantoms = [.. navigationFile.Phantoms.Select(p => p.Source)];
+		NavigationItems = BuildNavigation(navigationFile.TableOfContents, 0);
+
 		var navigationIndex = 0;
 		var allNavigationItems = new HashSet<INavigationItem>();
-		UpdateNavigationIndex(allNavigationItems, NavigationItems, null, ref navigationIndex);
+		UpdateParent(allNavigationItems, NavigationItems, null);
+		UpdateNavigationIndex(NavigationItems, ref navigationIndex);
 		TopLevelItems = NavigationItems.OfType<TableOfContentsTree>().Where(t => !t.Hidden).ToList();
 		NavigationLookup = TopLevelItems.ToDictionary(kv => kv.Source, kv => kv);
 
@@ -42,13 +58,13 @@ public GlobalNavigation(AssembleSources assembleSources, GlobalNavigationFile na
 			.SelectMany(DocumentationSet.Pairs)
 			.ToDictionary(kv => kv.Item1, kv => kv.Item2)
 			.ToFrozenDictionary();
+
 	}
 
-	private void UpdateNavigationIndex(
+	private void UpdateParent(
 		HashSet<INavigationItem> allNavigationItems,
 		IReadOnlyCollection<INavigationItem> navigationItems,
-		INodeNavigationItem<INavigationModel, INavigationItem>? parent,
-		ref int navigationIndex
+		INodeNavigationItem<INavigationModel, INavigationItem>? parent
 	)
 	{
 		foreach (var item in navigationItems)
@@ -56,19 +72,15 @@ ref int navigationIndex
 			switch (item)
 			{
 				case FileNavigationItem fileNavigationItem:
-					var fileIndex = Interlocked.Increment(ref navigationIndex);
-					fileNavigationItem.NavigationIndex = fileIndex;
 					if (parent is not null)
 						fileNavigationItem.Parent = parent;
 					_ = allNavigationItems.Add(fileNavigationItem);
 					break;
 				case DocumentationGroup documentationGroup:
-					var groupIndex = Interlocked.Increment(ref navigationIndex);
-					documentationGroup.NavigationIndex = groupIndex;
 					if (parent is not null)
 						documentationGroup.Parent = parent;
 					_ = allNavigationItems.Add(documentationGroup);
-					UpdateNavigationIndex(allNavigationItems, documentationGroup.NavigationItems, documentationGroup, ref navigationIndex);
+					UpdateParent(allNavigationItems, documentationGroup.NavigationItems, documentationGroup);
 					break;
 				default:
 					_navigationFile.EmitError($"Unhandled navigation item type: {item.GetType()}");
@@ -77,29 +89,57 @@ ref int navigationIndex
 		}
 	}
 
-	private IReadOnlyCollection<INavigationItem> BuildNavigation(IReadOnlyCollection<TocReference> node, int depth)
+
+	private void UpdateNavigationIndex(IReadOnlyCollection<INavigationItem> navigationItems, ref int navigationIndex)
+	{
+		foreach (var item in navigationItems)
+		{
+			switch (item)
+			{
+				case FileNavigationItem fileNavigationItem:
+					var fileIndex = Interlocked.Increment(ref navigationIndex);
+					fileNavigationItem.NavigationIndex = fileIndex;
+					break;
+				case DocumentationGroup documentationGroup:
+					var groupIndex = Interlocked.Increment(ref navigationIndex);
+					documentationGroup.NavigationIndex = groupIndex;
+					UpdateNavigationIndex(documentationGroup.NavigationItems, ref navigationIndex);
+					break;
+				default:
+					_navigationFile.EmitError($"Unhandled navigation item type: {item.GetType()}");
+					break;
+			}
+		}
+	}
+
+	private IReadOnlyCollection<INavigationItem> BuildNavigation(IReadOnlyCollection<TocReference> references, int depth)
 	{
 		var list = new List<INavigationItem>();
-		foreach (var toc in node)
+		foreach (var tocReference in references)
 		{
-			if (!_assembleSources.TreeCollector.TryGetTableOfContentsTree(toc.Source, out var tree))
+			if (!_assembleSources.TreeCollector.TryGetTableOfContentsTree(tocReference.Source, out var tree))
 			{
-				_navigationFile.EmitError($"{toc.Source} does not define a toc.yml or docset.yml file");
+				_navigationFile.EmitError($"{tocReference.Source} does not define a toc.yml or docset.yml file");
 				continue;
 			}
 
-			var navigationItem = tree;
-			var tocChildren = toc.Children.OfType<TocReference>().ToArray();
+			var tocChildren = tocReference.Children.OfType<TocReference>().ToArray();
 			var tocNavigationItems = BuildNavigation(tocChildren, depth + 1);
 
-			var allNavigationItems =
+			if (depth == 0 && tree.Parent != RootContentTree)
+			{
+				tree.Parent = RootContentTree;
+				tree.Index.NavigationRoot = tree;
+			}
+
+			var configuredNavigationItems =
 				depth == 0
 					? tocNavigationItems.Concat(tree.NavigationItems)
 					: tree.NavigationItems.Concat(tocNavigationItems);
 
 			var cleanNavigationItems = new List<INavigationItem>();
 			var seenSources = new HashSet<Uri>();
-			foreach (var item in allNavigationItems)
+			foreach (var item in configuredNavigationItems)
 			{
 				if (item is not TableOfContentsTree tocNav)
 				{
@@ -110,22 +150,43 @@ private IReadOnlyCollection<INavigationItem> BuildNavigation(IReadOnlyCollection
 				if (seenSources.Contains(tocNav.Source))
 					continue;
 
-				if (!_assembleSources.TocTopLevelMappings.TryGetValue(tocNav.Source, out var mapping))
+				if (Phantoms.Contains(tree.NavigationSource))
+					continue;
+
+				// toc is not part of `navigation.yml`
+				if (!_assembleSources.NavigationTocMappings.TryGetValue(tocNav.Source, out var mapping))
 					continue;
 
+				// this TOC was moved in navigation.yml to a new parent and should not be part of the current navigation items
 				if (mapping.ParentSource != tree.Source)
 					continue;
 
 				_ = seenSources.Add(tocNav.Source);
 				cleanNavigationItems.Add(item);
-				item.Parent = navigationItem;
+				item.Parent = tree;
 			}
 
 			tree.NavigationItems = cleanNavigationItems.ToArray();
-			list.Add(navigationItem);
+			list.Add(tree);
 
-			if (toc.IsPhantom)
-				navigationItem.Hidden = true;
+			if (tocReference.IsPhantom)
+				tree.Hidden = true;
+		}
+
+		if (depth != 0)
+			return list.ToArray().AsReadOnly();
+
+		// the root files of `docs-content://` are special they contain several special pages such as 404, archive, versions etc.
+		// we inject them forcefully here
+		if (!RootContentTree.NavigationItems.OfType<FileNavigationItem>().Any())
+			_navigationFile.EmitError($"Could not inject root file navigation items from: {RootContentTree.Source}.");
+		else
+		{
+			var filesAtRoot = RootContentTree.NavigationItems.OfType<FileNavigationItem>().ToArray();
+			list.AddRange(filesAtRoot);
+			// ensure index exist as a single item rather than injecting the whole tree (which already exists in the returned list)
+			var index = new FileNavigationItem(RootContentTree.Index, RootContentTree, RootContentTree.Hidden);
+			list.Add(index);
 		}
 
 		return list.ToArray().AsReadOnly();
diff --git a/src/tooling/docs-assembler/Navigation/GlobalNavigationHtmlWriter.cs b/src/tooling/docs-assembler/Navigation/GlobalNavigationHtmlWriter.cs
index 277636107..9a65dd4ad 100644
--- a/src/tooling/docs-assembler/Navigation/GlobalNavigationHtmlWriter.cs
+++ b/src/tooling/docs-assembler/Navigation/GlobalNavigationHtmlWriter.cs
@@ -3,95 +3,48 @@
 // See the LICENSE file in the project root for more information
 
 using System.Collections.Concurrent;
-using System.Collections.Immutable;
-using System.Diagnostics.CodeAnalysis;
-using Elastic.Documentation.Extensions;
 using Elastic.Documentation.Site.Navigation;
 using Elastic.Markdown.IO.Navigation;
+using Microsoft.Extensions.Logging;
 
 namespace Documentation.Assembler.Navigation;
 
-public class GlobalNavigationHtmlWriter(
-	GlobalNavigationFile navigationFile,
-	AssembleContext assembleContext,
-	GlobalNavigation globalNavigation,
-	AssembleSources assembleSources
-) : INavigationHtmlWriter
+public class GlobalNavigationHtmlWriter(ILoggerFactory logFactory, GlobalNavigation globalNavigation) : INavigationHtmlWriter
 {
-	private readonly ConcurrentDictionary<(Uri, int), string> _renderedNavigationCache = [];
+	private readonly ILogger<Program> _logger = logFactory.CreateLogger<Program>();
 
-	private ImmutableHashSet<Uri> Phantoms { get; } = [.. navigationFile.Phantoms.Select(p => p.Source)];
+	private readonly ConcurrentDictionary<(string, int), string> _renderedNavigationCache = [];
 
-	private bool TryGetNavigationRoot(
-		Uri navigationSource,
-		[NotNullWhen(true)] out TableOfContentsTree? navigationRoot,
-		[NotNullWhen(true)] out Uri? navigationRootSource
-	)
+	public async Task<NavigationRenderResult> RenderNavigation(IRootNavigationItem<INavigationModel, INavigationItem> currentRootNavigation, int maxLevel, Cancel ctx = default)
 	{
-		navigationRoot = null;
-		navigationRootSource = null;
-		if (!assembleSources.TocTopLevelMappings.TryGetValue(navigationSource, out var topLevelMapping))
+		INodeNavigationItem<INavigationModel, INavigationItem> lastParentBeforeRoot = currentRootNavigation;
+		INodeNavigationItem<INavigationModel, INavigationItem> parent = currentRootNavigation;
+		while (parent.Parent is not null)
 		{
-			if (assembleSources.TreeCollector.TryGetTableOfContentsTree(navigationSource, out navigationRoot))
-			{
-				if (navigationRoot.Parent is DocumentationGroup parent &&
-					assembleSources.TocTopLevelMappings.TryGetValue(parent.NavigationSource, out var topLevelMapping2))
-				{
-					navigationRootSource = topLevelMapping2.TopLevelSource;
-					return true;
-				}
-
-				assembleContext.Collector.EmitError(assembleContext.NavigationPath.FullName, $"The following toc: {navigationSource} is not declared in navigation.yml and it's parent failed to yield a navigation root.");
-				return false;
-			}
-			assembleContext.Collector.EmitError(assembleContext.NavigationPath.FullName, $"The following toc: {navigationSource} is not declared in navigation.yml");
-			return false;
+			lastParentBeforeRoot = parent;
+			parent = parent.Parent;
 		}
-
-		if (!assembleSources.TreeCollector.TryGetTableOfContentsTree(topLevelMapping.TopLevelSource, out navigationRoot))
-		{
-			assembleContext.Collector.EmitError(assembleContext.NavigationPath.FullName, $"None of the assemble sources define a toc for: {topLevelMapping.TopLevelSource}");
-			return false;
-		}
-		navigationRootSource = topLevelMapping.TopLevelSource;
-		return true;
-	}
-
-	public async Task<NavigationRenderResult> RenderNavigation(IRootNavigationItem<INavigationModel, INavigationItem> currentRootNavigation,
-		Uri navigationSource, int maxLevel, Cancel ctx = default)
-	{
-		if (Phantoms.Contains(navigationSource)
-			|| !TryGetNavigationRoot(navigationSource, out var navigationRoot, out var navigationRootSource)
-			|| Phantoms.Contains(navigationRootSource)
-		   )
-			return NavigationRenderResult.Empty;
-
-		var navigationId = ShortId.Create($"{(navigationRootSource, maxLevel).GetHashCode()}");
-
-		if (_renderedNavigationCache.TryGetValue((navigationRootSource, maxLevel), out var value))
+		if (_renderedNavigationCache.TryGetValue((lastParentBeforeRoot.Id, maxLevel), out var html))
 		{
 			return new NavigationRenderResult
 			{
-				Html = value,
-				Id = navigationId
+				Html = html,
+				Id = lastParentBeforeRoot.Id
 			};
 		}
 
-		if (navigationRootSource == new Uri("docs-content:///"))
-		{
-			_renderedNavigationCache[(navigationRootSource, maxLevel)] = string.Empty;
-			return NavigationRenderResult.Empty;
-		}
+		_logger.LogInformation("Rendering navigation for {NavigationTitle} ({Id})", lastParentBeforeRoot.NavigationTitle, lastParentBeforeRoot.Id);
 
-		Console.WriteLine($"Rendering navigation for {navigationRootSource}");
+		if (lastParentBeforeRoot is not DocumentationGroup group)
+			return NavigationRenderResult.Empty;
 
-		var model = CreateNavigationModel(navigationRoot, maxLevel);
-		value = await ((INavigationHtmlWriter)this).Render(model, ctx);
-		_renderedNavigationCache[(navigationRootSource, maxLevel)] = value;
+		var model = CreateNavigationModel(group, maxLevel);
+		html = await ((INavigationHtmlWriter)this).Render(model, ctx);
+		_renderedNavigationCache[(lastParentBeforeRoot.Id, maxLevel)] = html;
 		return new NavigationRenderResult
 		{
-			Html = value,
-			Id = navigationId
+			Html = html,
+			Id = lastParentBeforeRoot.Id
 		};
 	}
 
diff --git a/src/tooling/docs-assembler/Navigation/GlobalNavigationPathProvider.cs b/src/tooling/docs-assembler/Navigation/GlobalNavigationPathProvider.cs
index 04f156d64..b9c10a978 100644
--- a/src/tooling/docs-assembler/Navigation/GlobalNavigationPathProvider.cs
+++ b/src/tooling/docs-assembler/Navigation/GlobalNavigationPathProvider.cs
@@ -25,7 +25,7 @@ public GlobalNavigationPathProvider(GlobalNavigationFile navigationFile, Assembl
 		_assembleSources = assembleSources;
 		_context = context;
 
-		TableOfContentsPrefixes = [..assembleSources.TocTopLevelMappings
+		TableOfContentsPrefixes = [..assembleSources.NavigationTocMappings
 			.Values
 			.Select(p =>
 			{
@@ -91,7 +91,7 @@ public GlobalNavigationPathProvider(GlobalNavigationFile navigationFile, Assembl
 			break;
 		}
 
-		if (match is null || !_assembleSources.TocTopLevelMappings.TryGetValue(match, out var toc))
+		if (match is null || !_assembleSources.NavigationTocMappings.TryGetValue(match, out var toc))
 		{
 			if (relativePath.StartsWith("raw-migrated-files/", StringComparison.Ordinal))
 				return null;
diff --git a/tests/docs-assembler.Tests/src/docs-assembler.Tests/GlobalNavigationTests.cs b/tests/docs-assembler.Tests/src/docs-assembler.Tests/GlobalNavigationTests.cs
index 6ba63df13..23bedfdb9 100644
--- a/tests/docs-assembler.Tests/src/docs-assembler.Tests/GlobalNavigationTests.cs
+++ b/tests/docs-assembler.Tests/src/docs-assembler.Tests/GlobalNavigationTests.cs
@@ -106,7 +106,7 @@ public async Task PathProvider()
 		var navigationFile = new GlobalNavigationFile(Context, assembleSources);
 		var pathProvider = new GlobalNavigationPathProvider(navigationFile, assembleSources, Context);
 
-		assembleSources.TocTopLevelMappings.Should().NotBeEmpty().And.ContainKey(new Uri("detection-rules://"));
+		assembleSources.NavigationTocMappings.Should().NotBeEmpty().And.ContainKey(new Uri("detection-rules://"));
 		pathProvider.TableOfContentsPrefixes.Should().Contain("detection-rules://");
 	}
 
@@ -122,12 +122,12 @@ public async Task ParsesReferences()
 		var clients = new Uri("docs-content://reference/elasticsearch-clients/");
 		var assembleSources = await Setup();
 
-		assembleSources.TocTopLevelMappings.Should().NotBeEmpty().And.ContainKey(sut);
-		assembleSources.TocTopLevelMappings[sut].TopLevelSource.Should().Be(expectedRoot);
-		assembleSources.TocTopLevelMappings.Should().NotBeEmpty().And.ContainKey(expectedRoot);
-		assembleSources.TocTopLevelMappings[sut].ParentSource.Should().Be(expectedParent);
+		assembleSources.NavigationTocMappings.Should().NotBeEmpty().And.ContainKey(sut);
+		assembleSources.NavigationTocMappings[sut].TopLevelSource.Should().Be(expectedRoot);
+		assembleSources.NavigationTocMappings.Should().NotBeEmpty().And.ContainKey(expectedRoot);
+		assembleSources.NavigationTocMappings[sut].ParentSource.Should().Be(expectedParent);
 
-		assembleSources.TocTopLevelMappings.Should().NotBeEmpty().And.ContainKey(new Uri("detection-rules://"));
+		assembleSources.NavigationTocMappings.Should().NotBeEmpty().And.ContainKey(new Uri("detection-rules://"));
 
 		var navigationFile = new GlobalNavigationFile(Context, assembleSources);
 		var referenceToc = navigationFile.TableOfContents.FirstOrDefault(t => t.Source == expectedRoot);
@@ -193,9 +193,9 @@ public async Task ParsesGlobalNavigation()
 		var kibanaExtendMoniker = new Uri("kibana://extend/");
 
 		var assembleSources = await Setup();
-		assembleSources.TocTopLevelMappings.Should().NotBeEmpty().And.ContainKey(kibanaExtendMoniker);
-		assembleSources.TocTopLevelMappings[kibanaExtendMoniker].TopLevelSource.Should().Be(expectedRoot);
-		assembleSources.TocTopLevelMappings.Should().NotBeEmpty().And.ContainKey(new Uri("docs-content://reference/apm/"));
+		assembleSources.NavigationTocMappings.Should().NotBeEmpty().And.ContainKey(kibanaExtendMoniker);
+		assembleSources.NavigationTocMappings[kibanaExtendMoniker].TopLevelSource.Should().Be(expectedRoot);
+		assembleSources.NavigationTocMappings.Should().NotBeEmpty().And.ContainKey(new Uri("docs-content://reference/apm/"));
 
 		var uri = new Uri("integration-docs://reference/");
 		assembleSources.TreeCollector.Should().NotBeNull();