Shane,
Having grown up just east of Etna in Yreka, CA I think I give some decent advise on this. I will provide several options and some of these may be more economical than others.
The nearest signifcant airport from Etna is in Medford OR. You should be able to get flights into Medford, however, you might find them to be expensive. Medford is approximately 85 miles by car from Etna. Going further out, you will find airports in Sacramento, CA which is is about 250 miles from Etna. You will find large airports in both Oakland, CA and San Francisco, CA both of which are approximatley 380 miles from Etna.
Etna is located approximately 35 miles southeast of I-5, which is the major interstate Highway through CA, OR, WA.
If you can get the flight in and out of Medford, OR you should be able to hike for several weeks and than easily hitch back to Medford for your flight out. Depending upon your daily mileage you should definitely be able to make it at least to Crater Lake within 2 weeks.
From Medford you will be able to get Greyhound bus service between Medford and Yreka. From Yreka to Etna you can transfer to the Siskiyou Stage bus service. Check the links at http://www.co.siskiyou.ca.us/dpw/stage/stage_schedule.htm
for current bus schedule between Yreka and Scott Valley.
Your transportation back to Medford will be dependant upon where you get off-trail. You and your partner should make some general plans for mileage goals. Obviously your partner will have been hiking for the better part of 4 months and will likely be doing 20-25 mile days by this time. You may not be ready for this right off the bat so you will need to come up with shared goals if you are going to hike together.
Good luck.
Jeff