Can anyone help me find this Superman Story Arc?

I remember reading a comic back in middle school, so both the time period and what I remember of the art date it as mid 2000s. It starts off with him eating at a diner, then some basic plot stuff happens, when he finds a hatch down into a secret bunker filled with kryptonians. Also I think his das is there, but as a hologram. A lot of the kryptonians call him a baby and are taller than he is, and he can’t fly in the bunker city. They also don’t let him leave till the last issue.

I don’t know if it was a dedicated mini series or what but it was probably about 6 issues long, can anyone help?

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You might be thinking of the Return to Krypton storyline.

Another possibility is Godfall.

My Research Monkies are on the case!

Sounds a little like the Kryptonite arc in Superman/ Batman. They find the “last line” under the floor of a diner in Smallville. A rogue special ops group created to kill Supes & manufacturing Krytonite bullets & various weapons/ soldiers in Smallville prepared to kill Supes if he ever loses it. Nothing else fits your description tho, no holograms calling him a baby etc.