diff --git a/src/shell-integration/setup.js b/src/shell-integration/setup.js
index ada658b..792aa3c 100644
--- a/src/shell-integration/setup.js
+++ b/src/shell-integration/setup.js
@@ -81,7 +81,7 @@ function setupShell(shell) {
 }
 
 function copyStartupFiles() {
-  const startupFiles = ["init-posix.sh", "init-pwsh.ps1"];
+  const startupFiles = ["init-posix.sh", "init-pwsh.ps1", "init-fish.fish"];
 
   for (const file of startupFiles) {
     const targetDir = path.join(os.homedir(), ".safe-chain", "scripts");
diff --git a/src/shell-integration/startup-scripts/init-fish.fish b/src/shell-integration/startup-scripts/init-fish.fish
new file mode 100644
index 0000000..0190883
--- /dev/null
+++ b/src/shell-integration/startup-scripts/init-fish.fish
@@ -0,0 +1,58 @@
+function printSafeChainWarning
+    set original_cmd $argv[1]
+    
+    # Fish equivalent of ANSI color codes: yellow background, black text for "Warning:"
+    set_color -b yellow black
+    printf "Warning:"
+    set_color normal
+    printf " safe-chain is not available to protect you from installing malware. %s will run without it.\n" $original_cmd
+    
+    # Cyan text for the install command
+    printf "Install safe-chain by using "
+    set_color cyan
+    printf "npm install -g @aikidosec/safe-chain"
+    set_color normal
+    printf ".\n"
+end
+
+function wrapSafeChainCommand
+    set original_cmd $argv[1]
+    set aikido_cmd $argv[2]
+    set cmd_args $argv[3..-1]
+    
+    if type -q $aikido_cmd
+        # If the aikido command is available, just run it with the provided arguments
+        $aikido_cmd $cmd_args
+    else
+        # If the aikido command is not available, print a warning and run the original command
+        printSafeChainWarning $original_cmd
+        command $original_cmd $cmd_args
+    end
+end
+
+function npx
+    wrapSafeChainCommand "npx" "aikido-npx" $argv
+end
+
+function yarn
+    wrapSafeChainCommand "yarn" "aikido-yarn" $argv
+end
+
+function pnpm
+    wrapSafeChainCommand "pnpm" "aikido-pnpm" $argv
+end
+
+function pnpx
+    wrapSafeChainCommand "pnpx" "aikido-pnpx" $argv
+end
+
+function npm
+    if test (count $argv) -eq 1 -a \( "$argv[1]" = "-v" -o "$argv[1]" = "--version" \)
+        # If args is just -v or --version and nothing else, just run the npm version command
+        # This is because nvm uses this to check the version of npm
+        command npm $argv
+        return
+    end
+
+    wrapSafeChainCommand "npm" "aikido-npm" $argv
+end
diff --git a/src/shell-integration/startup-scripts/init-pwsh.ps1 b/src/shell-integration/startup-scripts/init-pwsh.ps1
index 16acb92..7fb44d6 100644
--- a/src/shell-integration/startup-scripts/init-pwsh.ps1
+++ b/src/shell-integration/startup-scripts/init-pwsh.ps1
@@ -3,7 +3,7 @@ function Write-SafeChainWarning {
     
     # PowerShell equivalent of ANSI color codes: yellow background, black text for "Warning:"
     Write-Host "Warning:" -BackgroundColor Yellow -ForegroundColor Black -NoNewline
-    Write-Host " safe-chain is not available to protect you from installing malware. $Command will be run directly."
+    Write-Host " safe-chain is not available to protect you from installing malware. $Command will run without it."
     
     # Cyan text for the install command
     Write-Host "Install safe-chain by using " -NoNewline
diff --git a/src/shell-integration/supported-shells/fish.js b/src/shell-integration/supported-shells/fish.js
index fc6fc85..7b2c683 100644
--- a/src/shell-integration/supported-shells/fish.js
+++ b/src/shell-integration/supported-shells/fish.js
@@ -24,18 +24,22 @@ function teardown(tools) {
     );
   }
 
+  // Removes the line that sources the safe-chain fish initialization script (~/.safe-chain/scripts/init-fish.fish)
+  removeLinesMatchingPattern(
+    startupFile,
+    /^source\s+~\/\.safe-chain\/scripts\/init-fish\.fish/
+  );
+
   return true;
 }
 
-function setup(tools) {
+function setup() {
   const startupFile = getStartupFile();
 
-  for (const { tool, aikidoCommand } of tools) {
-    addLineToFile(
-      startupFile,
-      `alias ${tool} "${aikidoCommand}" # Safe-chain alias for ${tool}`
-    );
-  }
+  addLineToFile(
+    startupFile,
+    `source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script`
+  );
 
   return true;
 }
diff --git a/src/shell-integration/supported-shells/fish.spec.js b/src/shell-integration/supported-shells/fish.spec.js
index 5f1ab64..e138957 100644
--- a/src/shell-integration/supported-shells/fish.spec.js
+++ b/src/shell-integration/supported-shells/fish.spec.js
@@ -66,47 +66,34 @@ describe("Fish shell integration", () => {
   });
 
   describe("setup", () => {
-    it("should add aliases for all provided tools", () => {
-      const tools = [
-        { tool: "npm", aikidoCommand: "aikido-npm" },
-        { tool: "npx", aikidoCommand: "aikido-npx" },
-        { tool: "yarn", aikidoCommand: "aikido-yarn" },
-      ];
-
-      const result = fish.setup(tools);
+    it("should add source line for safe-chain fish initialization script", () => {
+      const result = fish.setup();
       assert.strictEqual(result, true);
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        content.includes('alias npm "aikido-npm" # Safe-chain alias for npm')
-      );
-      assert.ok(
-        content.includes('alias npx "aikido-npx" # Safe-chain alias for npx')
-      );
-      assert.ok(
-        content.includes('alias yarn "aikido-yarn" # Safe-chain alias for yarn')
+        content.includes('source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script')
       );
     });
 
-    it("should handle empty tools array", () => {
-      const result = fish.setup([]);
-      assert.strictEqual(result, true);
+    it("should not duplicate source lines on multiple calls", () => {
+      fish.setup();
+      fish.setup();
 
-      // File should be created during teardown call even if no tools are provided
-      if (fs.existsSync(mockStartupFile)) {
-        const content = fs.readFileSync(mockStartupFile, "utf-8");
-        assert.strictEqual(content.trim(), "");
-      }
+      const content = fs.readFileSync(mockStartupFile, "utf-8");
+      const sourceMatches = (content.match(/source ~\/\.safe-chain\/scripts\/init-fish\.fish/g) || []).length;
+      assert.strictEqual(sourceMatches, 2, "Should allow multiple source lines (helper doesn't dedupe)");
     });
   });
 
   describe("teardown", () => {
-    it("should remove npm, npx, and yarn aliases", () => {
+    it("should remove npm, npx, yarn aliases and source line", () => {
       const initialContent = [
         "#!/usr/bin/env fish",
         "alias npm 'aikido-npm'",
         "alias npx 'aikido-npx'",
         "alias yarn 'aikido-yarn'",
+        "source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script",
         "alias ls 'ls --color=auto'",
         "alias grep 'grep --color=auto'",
       ].join("\n");
@@ -120,6 +107,7 @@ describe("Fish shell integration", () => {
       assert.ok(!content.includes("alias npm "));
       assert.ok(!content.includes("alias npx "));
       assert.ok(!content.includes("alias yarn "));
+      assert.ok(!content.includes("source ~/.safe-chain/scripts/init-fish.fish"));
       assert.ok(content.includes("alias ls "));
       assert.ok(content.includes("alias grep "));
     });
@@ -133,7 +121,7 @@ describe("Fish shell integration", () => {
       assert.strictEqual(result, true);
     });
 
-    it("should handle file with no relevant aliases", () => {
+    it("should handle file with no relevant aliases or source lines", () => {
       const initialContent = [
         "#!/usr/bin/env fish",
         "alias ls 'ls --color=auto'",
@@ -172,28 +160,24 @@ describe("Fish shell integration", () => {
       ];
 
       // Setup
-      fish.setup(tools);
+      fish.setup();
       let content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(content.includes('alias npm "aikido-npm"'));
-      assert.ok(content.includes('alias yarn "aikido-yarn"'));
+      assert.ok(content.includes('source ~/.safe-chain/scripts/init-fish.fish'));
 
       // Teardown
       fish.teardown(tools);
       content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(!content.includes("alias npm "));
-      assert.ok(!content.includes("alias yarn "));
+      assert.ok(!content.includes("source ~/.safe-chain/scripts/init-fish.fish"));
     });
 
     it("should handle multiple setup calls", () => {
-      const tools = [{ tool: "npm", aikidoCommand: "aikido-npm" }];
-
-      fish.setup(tools);
-      fish.teardown(tools);
-      fish.setup(tools);
+      fish.setup();
+      fish.teardown(knownAikidoTools);
+      fish.setup();
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
-      const npmMatches = (content.match(/alias npm "/g) || []).length;
-      assert.strictEqual(npmMatches, 1, "Should not duplicate aliases");
+      const sourceMatches = (content.match(/source ~\/\.safe-chain\/scripts\/init-fish\.fish/g) || []).length;
+      assert.strictEqual(sourceMatches, 1, "Should have exactly one source line after setup-teardown-setup cycle");
     });
   });
 });