Vitest working with Nitro v2, but not with Nitro v3.0.1-alpha.0

Environment

npx --yes envinfo --system --binaries

  System:
    OS: Linux 6.17 Arch Linux
    Container: Yes
    Shell: 5.9 - /usr/bin/zsh
  Binaries:
    Node: 24.10.0
    npm: 11.6.2
    pnpm: 10.18.3

Reproduction

https://github.com/theoludwig/vite-nitro-issues

Unfortunately this is not a "as minimal as possible reproduction", but I thought it was still worth to open the issue as an early tester of Nitro v3 alpha version, and that it was working with v2. The provided reproduction is a TanStack Start application following their documentation about Nitro usage: https://tanstack.com/start/latest/docs/framework/react/guide/hosting#using-nitro-v2

I haven't had time to investigate the issue further yet.

Describe the bug

node --run test which is using vitest run doesn't work with Nitro v3, but works with Nitro v2.

I did 2 commits in the reproduction example:

• chore: nitro v2 which use @tanstack/nitro-v2-vite-plugin and has a green CI, no problems.
• chore: nitro v3, with as you can see in the commit, the only change, is that it's using "nitro": "3.0.1-alpha.0", and the CI doesn't work (same behavior as locally), and fails with vitest run.

Additional context

No response

Logs

info Using tsconfig paths for react-docgen

⎯⎯⎯⎯⎯⎯⎯ Startup Error ⎯⎯⎯⎯⎯⎯⎯⎯
TypeError: Cannot read properties of undefined (reading 'onMessage')
    at Object.on (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/nitro@3.0.1-alpha.0_vite@7.1.10_@types+node@24.7.2_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6_/node_modules/nitro/dist/_chunks/plugin.mjs:348:13)
    at Object.setInvokeHandler (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/vite@7.1.10_@types+node@24.7.2_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6/node_modules/vite/dist/node/chunks/dep-B0GuR2De.js:28475:16)
    at new DevEnvironment (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/vite@7.1.10_@types+node@24.7.2_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6/node_modules/vite/dist/node/chunks/dep-B0GuR2De.js:35006:12)
    at new FetchableDevEnvironment (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/nitro@3.0.1-alpha.0_vite@7.1.10_@types+node@24.7.2_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6_/node_modules/nitro/dist/_chunks/plugin.mjs:318:5)
    at createFetchableDevEnvironment (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/nitro@3.0.1-alpha.0_vite@7.1.10_@types+node@24.7.2_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6_/node_modules/nitro/dist/_chunks/plugin.mjs:313:10)
    at Object.createEnvironment (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/nitro@3.0.1-alpha.0_vite@7.1.10_@types+node@24.7.2_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6_/node_modules/nitro/dist/_chunks/plugin.mjs:525:50)
    at _createServer (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/vite@7.1.10_@types+node@24.7.2_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6/node_modules/vite/dist/node/chunks/dep-B0GuR2De.js:27964:132)
    at async createViteServer (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/vitest@3.2.4_@types+node@24.7.2_@vitest+browser@3.2.4_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6/node_modules/vitest/dist/chunks/cli-api.BkDphVBG.js:6911:17)
    at async createVitest (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/vitest@3.2.4_@types+node@24.7.2_@vitest+browser@3.2.4_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6/node_modules/vitest/dist/chunks/cli-api.BkDphVBG.js:10202:17)
    at async prepareVitest (file:///home/runner/work/vite-nitro-issues/vite-nitro-issues/node_modules/.pnpm/vitest@3.2.4_@types+node@24.7.2_@vitest+browser@3.2.4_jiti@2.6.1_lightningcss@1.30.1_tsx@4.20.6/node_modules/vitest/dist/chunks/cli-api.BkDphVBG.js:10541:14)

Start with the linked vite-nitro-issues reproduction and compare the Nitro v2 and Nitro v3 commits. Run node --run test or vitest run, then inspect the Nitro plugin.mjs stack-trace path around the onMessage failure and Vite's setInvokeHandler. Done means the reproduction runs successfully with Nitro v3 without the startup error.