On this page of the game guide to Borderlands 2 you will find the walkthrough description of both of the parts of the main mission titled Where Angels Fear to Tread. The consecutive fragments of this mission will require you to visit the Sanctuary, Thousand Cuts and The Bunker.
3) Energy field
4) Gate 1
5) Gate 2
6) Badass Constructor
7) Passage to The Bunker
9) Cover from BNK3R's attacks
Accept the mission from Roland  and speak to Claptrap . Convincing him to help will turn out to be much easier than assumed. Use Fast Travel and head to the gate from the above screenshot, located in the south part of the map . Wait for Claptrap to switch off the field so you can safely head through.
Follow the road up, eliminating the Robots and Hyperion Soldiers that you come across. As you reach the end of the street, on your left you should notice a locked gate . In order to pass through, you will have to destroy a Constructor. Firstly take care of the turrets which it sets, as they can deal considerable damage.
Head through the open gate and Hyperion Soldiers will come out. Follow the road once again, avoiding the red markers on the ground, pointing where mortar fire will hit. As you reach the next gate , destroy the turrets on both sides of the gate.
Take a few steps behind the gate and on the upper part of the opposite building you should see a Badass Constructor . If you have a rocket launcher with a scope, try attacking it from as far as possible. After the fight, head to the passage leading to The Bunker .
Follow the path up. Use the Vending machines on the left to restock on ammo and head onwards. After reaching the main arena , destroy the Auto Cannon shown in the above screenshot. Afterwards you will have to destroy 11 more. They will be appearing around the bunker, some of them mounted on the ceiling/wall. An approximate location has been marked with dots on the map.
Sometimes lasers will appear on the map. As they turn on, jump onto the crates placed throughout the place.
After destroying all the Auto Cannons, the fight with BNK3R will appear. The boss will for most time keep flying around the arena, at a distance which will make it impossible to shoot at it. Often it will also place mines, as shown in the screenshot.
The boss should eventually hang in the air to shoot rockets at you. Hide behind a pillar  and destroy the turrets on its sides (square). For critical damage, aim at the spots marked with a circle. Keep repeating this each time BNK3R stops to fire another series of rockets.
After depriving the boss of 50% of its health, it will start using a bigger gun. Use the Robots which will appear on the arena for Second Wind. Sometimes ammunition will be dropped onto the arena as well. However if you will be still low on it, you can use the Vending machine by the entrance to the location.
After you destroy the robot, you will be able to use the passage on the lower level. Go through the scanning process and use the elevator to get to Control Core Angel. Use the button to open the entrance to Angel's room. Inside, land a few shots on the Eridium Injector.
Eridium Injectors will be surrounded by a shield and Robots, Core Defense Turrets (above the shield protecting Angel) and Shock Field Generators will start appearing in the room. The latter ones have to be destroyed as fast as possible, at best from a safe distance. Ammo crates will also appear around the field protecting Angel. After some time, Roland will also join the fight. If you last long enough, Roland should remove the shield from one of the Eridium Injectors. Destroy it.
Destroy enough Robots and Roland will start removing another Eridium Injector shield. Once again fight off the Robots to destroy another unprotected Eridium Injector. Now Lilith will also join the fight and help you remove the last shield.
With the last Eridium Injector destroyed, approach Angel and finish the first part of the mission by speaking with Roland. After the cutscene, you will find yourself in Sanctuary, at the back of Marcus' shop. Open all the crates which you find here. Head out of the room and return to Mordecai  to end the mission.