1. You find yourself aboard a packet transport (a kind of train). Ma3a instructs you to find a place to stow away.
2. You have entered another area (System Reboot from Legacy Code). Time to reconfigure memory.
3. ICPs spot you almost instantly. Clear out the immediate area and you'll find Permission 1, Permission 3, and a Gold Profiler (you have Beta) in their core dumps.
4. Miss Thang (er, um, Marcella) provides the 411 on the increased number of ICPs.
5. You are on car 1, upper level, port (left) side. These archive bins contain an email, Permission 1 (which you already have) and an Alpha Cluster.
6. Descend this ramp to the lower level.
7. Talk to J.J. -- he knows where you can stow away. "Head to the back of the transport and climb up. It's as simple as that." Yeah, right.
8. Head up the starboard ramp. Grab Permission 6 and use the infinite energy patch routine. Pass through the red door.
9. Build note 30 lifts you to v3.8.9. Backtrack through the door behind you.
10. Snatch build note 31 to raise your version to v3.9.1.
11. Head back down the ramp. Ready your weapon.
12. Defeat any ICPs in the area and grab their core dumps for health and energy.
13. Pass through this door. The archive bin on the right holds Permission 3 (which you have) and unknown subroutines that turn out to be an Alpha Support Safeguard and a Beta Fuzzy Signature, both of which you also have -- save your energy.
14. Build note 32 lifts you to v3.9.3. Continue through the right door.
15. You are now on car 2, lower level, starboard (right) side. Here's a health patch routine.
16. Beware the finder and ICPs patrolling here.
17. This area is a maze puzzle. Follow the arrows. Use the health patch routine in the first quadrant for reference.
18. Here's your reward -- an email and Permission 2.
19. Backtrack to here, where you can climb to the upper level. One of the ICPs up here is holding Permission 4, which you can also grab from an archive bin in Step 21.
20. Beware the finder patrolling this area. Drop back down to the lower level where you see build note 33.
21. Also down here is this archive bin, with Permission 4 and an Alpha Base Damping subroutine. You already have a Beta Triangulate subroutine.
22. Exit the car through either of these doors.
23. Continue to car 3 through either of the lower doors.
24. Ready your weapon before entering car 3, as there are many ICPs within.
25. If you allow the sec rezzer to call in this ICP, you can grab Permission 8 from his core dump, which is required to deactivate the sec rezzers (a bit late in the level for that though). Permission 8 also opens a useless door in step 30. You can grab Permissions 5 and 7 from the other ICPs, and regenerate at the car's patch routines.
26. Continue through either of the lower doors. (This archive bin containing Permission 5 is by the port-side door).
27. Miguel advises that you hide on the upper deck.
28. Ascend the ramp on the port side of the train.
29. These archive bins contain an email and an unknown subroutine, which turns out to be something you already have - a Beta Suffusion.
30. Build note 34 brings you to v3.9.7. The door seen here can only be opened with Permission 8, but there is nothing of interest behind it anyway.
31. Return below then head up the starboard ramp.
32. Up here you'll find this archive bin holding nothing you need - Permission 7, a Gold Profiler, and a Beta Y-Amp.
33. Through the door toward the train's front (inset) you'll find this Code Optimization Ware. Upgrade the subroutine of your preference. The Ball Launcher is a good choice and is upgraded to Beta for this walkthrough.
34. The opposite door is the level exit.
35. The cutscene shows you safely stowed aboard the tug.