diff --git a/.changeset/forty-pens-sip.md b/.changeset/forty-pens-sip.md
new file mode 100644
index 0000000..2b3ab8f
--- /dev/null
+++ b/.changeset/forty-pens-sip.md
@@ -0,0 +1,5 @@
+---
+"@khanacademy/graphql-flow": patch
+---
+
+Fix up some more alias resolution in graphql-flow.
diff --git a/schema.json b/schema.json
index 7c8df45..70d0b29 100644
--- a/schema.json
+++ b/schema.json
@@ -91,7 +91,23 @@
         "generate": {"oneOf": [
             {"$ref": "#/definitions/GenerateConfig"},
             {"type": "array", "items": {"$ref": "#/definitions/GenerateConfig"}}
-        ]}
+        ]},
+        "alias": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "additionalProperties": false,
+                "properties": {
+                    "find": {
+                        "type": ["string", "object"]
+                    },
+                    "replacement": {
+                        "type": "string"
+                    }
+                },
+                "required": [ "find", "replacement" ]
+            }
+        }
     },
     "required": [ "crawl", "generate" ]
-}
\ No newline at end of file
+}
diff --git a/src/cli/run.ts b/src/cli/run.ts
index f56d0ce..9c1190f 100644
--- a/src/cli/run.ts
+++ b/src/cli/run.ts
@@ -6,6 +6,7 @@ import type {GraphQLSchema} from "graphql/type/schema";
 import {generateTypeFiles, processPragmas} from "../generateTypeFiles";
 import {processFiles} from "../parser/parse";
 import {resolveDocuments} from "../parser/resolve";
+import {getPathWithExtension} from "../parser/utils";
 import {findApplicableConfig, getSchemas, loadConfigFile} from "./config";
 
 import {addTypenameToDocument} from "apollo-utilities";
@@ -81,22 +82,11 @@ const inputFiles = cliFiles.length
 /** Step (2) */
 
 const files = processFiles(inputFiles, config, (f) => {
-    if (existsSync(f)) {
-        return readFileSync(f, "utf8");
+    const resolvedPath = getPathWithExtension(f, config);
+    if (!resolvedPath) {
+        throw new Error(`Unable to find ${f}`);
     }
-    if (existsSync(f + ".js")) {
-        return {text: readFileSync(f + ".js", "utf8"), resolvedPath: f + ".js"};
-    }
-    if (existsSync(f + ".ts")) {
-        return {text: readFileSync(f + ".ts", "utf8"), resolvedPath: f + ".ts"};
-    }
-    if (existsSync(f + ".tsx")) {
-        return {
-            text: readFileSync(f + ".tsx", "utf8"),
-            resolvedPath: f + ".tsx",
-        };
-    }
-    throw new Error(`Unable to find ${f}`);
+    return {text: readFileSync(resolvedPath, "utf8"), resolvedPath};
 });
 
 let filesHadErrors = false;
diff --git a/src/parser/__test__/utils.test.ts b/src/parser/__test__/utils.test.ts
index 607d972..a8da61d 100644
--- a/src/parser/__test__/utils.test.ts
+++ b/src/parser/__test__/utils.test.ts
@@ -50,7 +50,7 @@ describe("getPathWithExtension", () => {
         expect(result).toBe("/path/to/file.js");
     });
 
-    it("returns an empty string if no file is found", () => {
+    it("returns null if no file is found", () => {
         // Arrange
         jest.spyOn(fs, "existsSync").mockImplementation((path) => false);
 
@@ -58,7 +58,7 @@ describe("getPathWithExtension", () => {
         const result = getPathWithExtension("/path/to/file", config);
 
         // Assert
-        expect(result).toBe("");
+        expect(result).toBe(null);
     });
 
     it("maps aliases to their correct value", () => {
diff --git a/src/parser/parse.ts b/src/parser/parse.ts
index da6e439..eac9e1b 100644
--- a/src/parser/parse.ts
+++ b/src/parser/parse.ts
@@ -11,7 +11,7 @@ import traverse from "@babel/traverse";
 
 import path from "path";
 
-import {getPathWithExtension} from "./utils";
+import {fixPathResolution, getPathWithExtension} from "./utils";
 import {Config} from "../types";
 
 /**
@@ -152,6 +152,7 @@ export const processFile = (
               text: string;
               resolvedPath: string;
           },
+    config: Config,
 ): FileResult => {
     const dir = path.dirname(filePath);
     const result: FileResult = {
@@ -177,7 +178,7 @@ export const processFile = (
 
     ast.program.body.forEach((toplevel) => {
         if (toplevel.type === "ImportDeclaration") {
-            const newLocals = getLocals(dir, toplevel, filePath);
+            const newLocals = getLocals(dir, toplevel, filePath, config);
             if (newLocals) {
                 Object.keys(newLocals).forEach((k) => {
                     const local = newLocals[k];
@@ -386,6 +387,7 @@ const getLocals = (
     dir: string,
     toplevel: ImportDeclaration,
     myPath: string,
+    config: Config,
 ):
     | {
           [key: string]: Import;
@@ -395,9 +397,10 @@ const getLocals = (
     if (toplevel.importKind === "type") {
         return null;
     }
-    const importPath = toplevel.source.value.startsWith(".")
-        ? path.resolve(path.join(dir, toplevel.source.value))
-        : toplevel.source.value;
+    const fixedPath = fixPathResolution(toplevel.source.value, config);
+    const importPath = fixedPath.startsWith(".")
+        ? path.resolve(path.join(dir, fixedPath))
+        : fixedPath;
     const locals: Record<string, any> = {};
     toplevel.specifiers.forEach((spec) => {
         if (spec.type === "ImportDefaultSpecifier") {
@@ -439,7 +442,7 @@ export const processFiles = (
         if (!next || files[next]) {
             continue;
         }
-        const result = processFile(next, getFileSource(next));
+        const result = processFile(next, getFileSource(next), config);
         files[next] = result;
         listExternalReferences(result, config).forEach((path) => {
             if (!files[path] && !toProcess.includes(path)) {
diff --git a/src/parser/resolve.ts b/src/parser/resolve.ts
index 03df2cb..f530a3d 100644
--- a/src/parser/resolve.ts
+++ b/src/parser/resolve.ts
@@ -51,7 +51,10 @@ const resolveImport = (
     },
     config: Config,
 ): Document | null | undefined => {
-    const absPath: string = getPathWithExtension(expr.path, config);
+    const absPath = getPathWithExtension(expr.path, config);
+    if (!absPath) {
+        return null;
+    }
     if (seen[absPath]) {
         errors.push({
             loc: expr.loc,
diff --git a/src/parser/utils.ts b/src/parser/utils.ts
index d0c7eb0..620157c 100644
--- a/src/parser/utils.ts
+++ b/src/parser/utils.ts
@@ -1,19 +1,20 @@
 import fs from "fs";
 import {Config} from "../types";
 
-export const getPathWithExtension = (
-    pathWithoutExtension: string,
-    config: Config,
-): string => {
-    // Process the path so that we can handle aliases.
+export const fixPathResolution = (path: string, config: Config) => {
     if (config.alias) {
         for (const {find, replacement} of config.alias) {
-            pathWithoutExtension = pathWithoutExtension.replace(
-                find,
-                replacement,
-            );
+            path = path.replace(find, replacement);
         }
     }
+    return path;
+};
+
+export const getPathWithExtension = (
+    pathWithoutExtension: string,
+    config: Config,
+) => {
+    pathWithoutExtension = fixPathResolution(pathWithoutExtension, config);
     if (
         /\.(less|css|png|gif|jpg|jpeg|js|jsx|ts|tsx|mjs)$/.test(
             pathWithoutExtension,
@@ -33,9 +34,5 @@ export const getPathWithExtension = (
     if (fs.existsSync(pathWithoutExtension + ".ts")) {
         return pathWithoutExtension + ".ts";
     }
-    // NOTE(john): This is a bit of a hack, but it's necessary for when we
-    // have a file that doesn't exist. This will happen when we delete all of
-    // the type files before re-running graphql-flow again. We want to ensure
-    // that we don't error out in this case.
-    return "";
+    return null;
 };