First you must click the model of a plant cell. This will give you cell dollars (shown at the bottom of the screen). Once you have some cell dollars, click the shop button in the bottom left to open the shop. You will then be able to purchase any of 12 different upgrades, each themed around a different cell part. As you hover over each upgrade, you can see the cost at the top of the screen, as well as a window showing the name of the cell part, its function, the upgrade to gain per second it provides, and its current multiplier to its profits. After you have gotten many of the last upgrade, don't quit yet! Once you have enough cell dollars, the purple rebirth button will appear at the bottom of the shop page, along with the name of one upgrade. When you purchase this upgrade, it will reset all of your progress, but increase the multiplier of whichever upgrade was displayed. The lower level upgrades are more likely to appear for the rebirth upgrade. To complete the game, reach a multiplier of 250x on all of the upgrades.
If you have any questions, suggestions, or have spotted any errors/bugs, please comment them on the project. All feedback is appreciated!