Been playing it more and think I finally understand how Robotics;Notes is structured. Each phase, after the first three which serve as prologue, is like a small episode with its own intro and ending credits. It's like you're watching a TV series.
The bizarre thing is, that the game refuses to let you just play them in order, despite the narrative only making sense if you do play them in order. What it expects you to do, is go back to a point in the game that acts as the starting hub of each of these episodes.
So you play for example Phase 6, then go back to Phase 5, do some weird thing, and only then does it jump to Phase 7. And repeat that process for Phases 7, and 8.
No idea why Mages decided to go with this system, after the pretty normal structure in Steins;Gate. Well, as long as you play with a walk-through, telling you exactly what weird things you need to do to play the game in order, it's pretty ok.
Actually story is pretty good, just very poor pacing that hurts it at times. This games shows very clearly how less is usually more when it comes to effective writing.