Take care of bugs in transit system is a mission in Daxter. After restoring pressure to the taps in the brewery, the Barmaid mentioned a worker from the transit system who said there were some bugs chewing though some electrical wires. Daxter then went to investigate on his own, ultimately running into a hive queen.
As with earlier areas, the transit system is fairly linear in nature with almost no real deviations from the main path aside from some collectibles. As such, follow the only possible route until you run into a new enemy known as a metal klaw. These scorpion-like metal bugs use their sawblades to charge at their targets with great speed. Use of the pressure boost attachment to evade them is recommended. Afterward, continue until you reach a part where a train continuously comes from the left and blocks your path; you will have to hover across. Keep in mind the track is electrified, so touching it (or the train) results in instant death.
In the next room is a rail which you must use as a zip line, which then takes you directly above a subway train. You have no choice but to drop down and begin train surfing while dodging panels and beams of electricity. Keep watch as the train enters larger and open areas, as this indicates another train will move past yours and that you will have to jump. This is to be done once early on, twice more later on and another two times after to reach a parked cargo train.
After moving through more small corridors and fighting bugs, you will run into a large cylindrical machine with rings of energy leading from the bottom to the top. The walls can be climbed and you must use them to head to the top, waiting at safe zones indicated by a blue light to avoid the energy rings. Several more corridors, paths, and tunnels filled with bugs await you until you reach another train surfing section. This one is quite long, and at the end you will have to hover across a large section of the tracks with two trains periodically racing past.
At the end is a service zoomer which you must borrow. As you start driving, a train appears and you must avoid slowing down by using booster pads and dodging the panels that are placed intermittently along the walls. The train crashes into a dead end at the tunnel. You can park the zoomer and use a nearby door with a green gas drafting outwards, leading into the first "Defeat hive queen" mission.