It is not possible to bundle Node.js modules into a single file with the TypeScript compiler alone: each file in the CommonJS module system (used by Node.js) is treated as a single module, and cannot be joined together without proper module bundling techniques found in the many JavaScript code bundlers out there (such as Browserify, Webpack, Rollup, Parceljs, …).
Other module systems such as SystemJS do not have this limitation, and module definitions can be concatenated into a single file using just the TypeScript compiler: tsc ... --outfile bundle.js -module system. However, they are not supported by Node.js on the fly.
For the actual solution, there are two reasonable choices: either configure your project to bundle the solution using a separate tool (Browserify, Webpack, …), or include an implementation of SystemJS into your Node.js application (instructions here).
I will also end with a side note: consider evaluating whether you really need to bundle your server-sided code. Bundling is typically performed in frontend projects to reduce the size of client-sided resources, although it can be done as well for server applications in resource-efficient scenarios.