diff --git a/internal/godocfx/index.go b/internal/godocfx/index.go
index 3cc418b8548..83ec59dbdde 100644
--- a/internal/godocfx/index.go
+++ b/internal/godocfx/index.go
@@ -28,7 +28,7 @@ import (
 
 // indexer gets a limited list of entries from index.golang.org.
 type indexer interface {
-	get(prefix string, since time.Time) (entries []indexEntry, last time.Time, err error)
+	get(prefixes []string, since time.Time) (entries []indexEntry, last time.Time, err error)
 }
 
 // indexClient is used to access index.golang.org.
@@ -49,7 +49,7 @@ type indexEntry struct {
 // versions since the given timestamp.
 //
 // newModules stores the timestamp of the last successful run with tSaver.
-func newModules(ctx context.Context, i indexer, tSaver timeSaver, prefix string) ([]indexEntry, error) {
+func newModules(ctx context.Context, i indexer, tSaver timeSaver, prefixes []string) ([]indexEntry, error) {
 	since, err := tSaver.get(ctx)
 	if err != nil {
 		return nil, err
@@ -61,7 +61,7 @@ func newModules(ctx context.Context, i indexer, tSaver timeSaver, prefix string)
 	for {
 		count++
 		var cur []indexEntry
-		cur, since, err = i.get(prefix, since)
+		cur, since, err = i.get(prefixes, since)
 		if err != nil {
 			return nil, err
 		}
@@ -80,7 +80,7 @@ func newModules(ctx context.Context, i indexer, tSaver timeSaver, prefix string)
 
 // get fetches a single chronological page of modules from
 // index.golang.org/index.
-func (indexClient) get(prefix string, since time.Time) ([]indexEntry, time.Time, error) {
+func (indexClient) get(prefixes []string, since time.Time) ([]indexEntry, time.Time, error) {
 	entries := []indexEntry{}
 	sinceString := since.Format(time.RFC3339)
 	resp, err := http.Get("https://index.golang.org/index?since=" + sinceString)
@@ -96,7 +96,7 @@ func (indexClient) get(prefix string, since time.Time) ([]indexEntry, time.Time,
 			return nil, time.Time{}, err
 		}
 		last = e.Timestamp // Always update the last timestamp.
-		if !strings.HasPrefix(e.Path, prefix) ||
+		if !hasPrefix(e.Path, prefixes) ||
 			strings.Contains(e.Path, "internal") ||
 			strings.Contains(e.Path, "third_party") ||
 			strings.Contains(e.Version, "-") { // Filter out pseudo-versions.
diff --git a/internal/godocfx/index_test.go b/internal/godocfx/index_test.go
index 35ad813235a..db1e0b3ef97 100644
--- a/internal/godocfx/index_test.go
+++ b/internal/godocfx/index_test.go
@@ -26,7 +26,7 @@ const wantEntries = 5
 
 type fakeIC struct{}
 
-func (f fakeIC) get(prefix string, since time.Time) (entries []indexEntry, last time.Time, err error) {
+func (f fakeIC) get(prefixes []string, since time.Time) (entries []indexEntry, last time.Time, err error) {
 	e := indexEntry{Timestamp: since.Add(24 * time.Hour)}
 	return []indexEntry{e}, e.Timestamp, nil
 }
@@ -49,7 +49,7 @@ func (f *fakeTS) put(context.Context, time.Time) error {
 func TestNewModules(t *testing.T) {
 	ic := fakeIC{}
 	ts := &fakeTS{}
-	entries, err := newModules(context.Background(), ic, ts, "cloud.google.com")
+	entries, err := newModules(context.Background(), ic, ts, []string{"cloud.google.com"})
 	if err != nil {
 		t.Fatalf("newModules got err: %v", err)
 	}
diff --git a/internal/godocfx/main.go b/internal/godocfx/main.go
index b9fc2aa2565..73cf4092e56 100644
--- a/internal/godocfx/main.go
+++ b/internal/godocfx/main.go
@@ -58,42 +58,43 @@ func main() {
 	outDir := flag.String("out", "obj/api", "Output directory (default obj/api)")
 	projectID := flag.String("project", "", "Project ID to use. Required when using -new-modules.")
 	newMods := flag.Bool("new-modules", false, "Process all new modules with the given prefix. Uses timestamp in Datastore. Stores results in $out/$mod.")
+	// TODO: flag to set output URL path
 
 	log.SetPrefix("[godocfx] ")
 
 	flag.Parse()
-	if flag.NArg() != 1 {
+	if flag.NArg() == 0 {
 		log.Fatalf("%s missing required argument: module path/prefix", os.Args[0])
 	}
 
-	mod := flag.Arg(0)
+	modNames := flag.Args()
 	var mods []indexEntry
 	if *newMods {
 		if *projectID == "" {
 			log.Fatal("Must set -project when using -new-modules")
 		}
 		var err error
-		mods, err = newModules(context.Background(), indexClient{}, &dsTimeSaver{projectID: *projectID}, mod)
+		mods, err = newModules(context.Background(), indexClient{}, &dsTimeSaver{projectID: *projectID}, modNames)
 		if err != nil {
 			log.Fatal(err)
 		}
 	} else {
-		modPath := mod
-		version := "latest"
-		if strings.Contains(mod, "@") {
-			parts := strings.Split(mod, "@")
-			if len(parts) != 2 {
-				log.Fatal("module arg expected only one '@'")
+		for _, mod := range modNames {
+			modPath := mod
+			version := "latest"
+			if strings.Contains(mod, "@") {
+				parts := strings.Split(mod, "@")
+				if len(parts) != 2 {
+					log.Fatal("module arg expected only one '@'")
+				}
+				modPath = parts[0]
+				version = parts[1]
 			}
-			modPath = parts[0]
-			version = parts[1]
-		}
-		modPath = strings.TrimSuffix(modPath, "/...") // No /... needed.
-		mods = []indexEntry{
-			{
+			modPath = strings.TrimSuffix(modPath, "/...") // No /... needed.
+			mods = append(mods, indexEntry{
 				Path:    modPath,
 				Version: version,
-			},
+			})
 		}
 	}
 
@@ -105,21 +106,19 @@ func main() {
 		return
 	}
 	// Create a temp module so we can get the exact version asked for.
-	tempDir, err := ioutil.TempDir("", "godocfx-*")
+	workingDir, err := ioutil.TempDir("", "godocfx-*")
 	if err != nil {
 		log.Fatalf("ioutil.TempDir: %v", err)
 	}
-	runCmd(tempDir, "go", "mod", "init", "cloud.google.com/go/lets-build-some-docs")
+	// Use a fake module that doesn't start with cloud.google.com/go.
+	runCmd(workingDir, "go", "mod", "init", "cloud.google.com/lets-build-some-docs")
 	for _, m := range mods {
 		log.Printf("Processing %s@%s", m.Path, m.Version)
 
-		path := *outDir
-		// If we have more than one module, we need a more specific out path.
-		if len(mods) > 1 {
-			path = filepath.Join(path, fmt.Sprintf("%s@%s", m.Path, m.Version))
-		}
-		if err := process(m, tempDir, path, *print); err != nil {
-			log.Printf("Failed to process %v", m)
+		// Always output to specific directory.
+		path := filepath.Join(*outDir, fmt.Sprintf("%s@%s", m.Path, m.Version))
+		if err := process(m, workingDir, path, *print); err != nil {
+			log.Printf("Failed to process %v: %v", m, err)
 		}
 		log.Printf("Done with %s@%s", m.Path, m.Version)
 	}
@@ -138,22 +137,23 @@ func runCmd(dir, name string, args ...string) error {
 	return nil
 }
 
-func process(mod indexEntry, tempDir, outDir string, print bool) error {
+func process(mod indexEntry, workingDir, outDir string, print bool) error {
 	// Be sure to get the module and run the module loader in the tempDir.
-	if err := runCmd(tempDir, "go", "mod", "tidy"); err != nil {
-		return err
+	if err := runCmd(workingDir, "go", "mod", "tidy"); err != nil {
+		return fmt.Errorf("go mod tidy error: %v", err)
 	}
-	if err := runCmd(tempDir, "go", "get", mod.Path+"@"+mod.Version); err != nil {
-		return err
+	if err := runCmd(workingDir, "go", "get", "-d", "-t", mod.Path+"/...@"+mod.Version); err != nil {
+		return fmt.Errorf("go get %s@%s: %v", mod.Path, mod.Version, err)
 	}
 
+	log.Println("Starting to parse")
 	optionalExtraFiles := []string{}
 	filter := []string{
 		"cloud.google.com/go/analytics",
 		"cloud.google.com/go/area120",
 		"cloud.google.com/go/gsuiteaddons",
 	}
-	r, err := parse(mod.Path+"/...", tempDir, optionalExtraFiles, filter)
+	r, err := parse(mod.Path+"/...", workingDir, optionalExtraFiles, filter)
 	if err != nil {
 		return fmt.Errorf("parse: %v", err)
 	}
diff --git a/internal/godocfx/parse.go b/internal/godocfx/parse.go
index 586c210c35b..e46677c2c68 100644
--- a/internal/godocfx/parse.go
+++ b/internal/godocfx/parse.go
@@ -452,8 +452,6 @@ func (l *linker) linkify(s string) string {
 	return fmt.Sprintf("%s%s.%s", prefix, href(l.toURL(pkgPath, ""), pkg), href(l.toURL(pkgPath, name), name))
 }
 
-// TODO: link to the right baseURL, with the right module name and version
-// pattern.
 func (l *linker) toURL(pkg, name string) string {
 	if pkg == "" {
 		if anchor := l.idToAnchor[""][name]; anchor != "" {
@@ -467,6 +465,7 @@ func (l *linker) toURL(pkg, name string) string {
 			pkgRemainder = pkg[len(mod.Path)+1:] // +1 to skip slash.
 		}
 		// Note: we always link to latest. One day, we'll link to mod.Version.
+		// Also, other packages may have different paths.
 		baseURL := fmt.Sprintf("/go/docs/reference/%v/latest/%v", mod.Path, pkgRemainder)
 		if anchor := l.idToAnchor[pkg][name]; anchor != "" {
 			return fmt.Sprintf("%s#%s", baseURL, anchor)