The OS of the RPi runs on an SD card. Only insert or remove this card when RPi is turned off (i.e., when it is not powered).
Make sure you back up your files. It is possibly that the file system of the RPi gets corrupted and that you need to reinstall your OS, in which case you lose all your data.
You can connect the RPi to a monitor via HDMI and a keyboard and mouse through USB. This way, you can work with it as any desktop computer. How to access the RPI in desktop mode is discussed in RPi in Desktop Mode.
The first thing you probably want to do is to connect the RPi to the UCSD Protected Wifi network. You do this by opening a terminal window, navigating to the Desktop from the command line and then executing the script "connect-to-wifi.sh" in sudo mode. This involves the following steps:
Click on the terminal icon in the top menu bar (the black icon of a computer window)
Type the following command: sudo bin/connect-wifi-fresh.sh
Follow the prompts for your Wifi ID and password. When asked if you want to reboot, answer 'y'. Your computer will reboot and hopefully connect to the UCSD Wifi.
It is also convenient to access the RPi remotely. For example, when the RPi is integrated into a robot, it is much harder to connect a keyboard and a monitor. This is explained in Remote Access. However, before you can connect remotely, you must configure the RPi first, which you need to do in desktop mode, so check that out first. Even if you do not have external peripherals available (monitor, mouse and keyboard), you still need to do this configuration in desktop mode, and we will explain there how can do this.