Your goal for the midgame is to acquire a Beacon. This is easier said than done however, because the recipe for it requires you to have progressed to Botania's endgame.

With the runes you learned to craft earlier, you can start upgrading your mana production, and start working towards Terrasteel.
For Terrasteel you will need a Terrestrial Agglomeration Plate. For details, check NEI.

With this Terrasteel, and an Aura Cascade Vortex Infusion setup, you can create Natura Pylons, which are one component of the Elven Gateway Portal.

The other component, the Elven Gateway Core, will require you to have been to the Witchery Dream World to acquire a Brew Of Hollow Tears.
Furthermore it will require you to get an Aura Cascade Arcane Prism. For info on how to get this, check the Encyclopedia Aura.

This will finally allow you to build the Elven Gateway Portal, which gives you access to Pixie Dust, which you need to craft a Beacon, and progress into the endgame.