If you choose ally after the control room, you are faced with several lock situations.
Also, once you have gotten to the end of all of this, be sure to go back and solve all puzzle rooms in Hard Mode. You don't need to re-solve any of the puzzles, because you already know the escape password, so just switch to Hard Mode and enter the escape passwords into the safes that you learned earlier. You don't need to have all of the archives for this.
Once you have solved all of the puzzle rooms on hard mode, check the flow chart for an extra ending.