My 1997 Saturn SW1 will not shift into 2nd, 3rd,

How does your transmission fluid look and smell? If it is dark and smells a little burnt, the transmission is very likely toast. If it is still clear and red, you should let a transmission specialist diagnose it.

sounds like a stretched linkage cable

Check the fluid level in you slave cylinder. If the fluid is low or there is air in the system it can cause hard shifting. If everything is ok it is problably the syncros.

http://techauto.awardspace.com/transmission.html
this covers the symptoms and the repairs. to me it sounds like it could be the tcu. maybe a blown capacitor. hope this helps. and goodluck.

If you have inspected the shift linkage and found no missing or loose parts, then unfortunately an internal shift mode fork, syncro assembly,shift rail or possibly a snap ring has been damaged. This is not an easy fix on any vehicle and will require transmission removal to diagnose. Before the trans is removed, inspect the shift linkage while someone moves the gear selector to all gears. This would be the best case scenario, internal damage, of course, would be the worst.

Howie I would go to a parts store or ebay and get a saturn shifter bushing repair kit. They cost about
20 bucks. If you can get the console out, then you can do this repair. If you have high speed access take a search on www.youtube.com for saturn shifter and i am sure there are videos of folks pulling the console and doing the bushing swap.

no hydralic fluid in the resvoir look for the resvoir on the fire wall of the drivers side if its empty well fill it back up lol not sure if the sw1 has this but ive had too fix this problem before

The clonk sounds like you have a loose nut on the mainshaft of your transmission, I don't have an article on it yet, but for now you can also check these 2:
Reverse slam fix
Swapping a Valve body on Saturn TAAT transaxle

I will have an article on how to tighten the mainaxle nut shortly
Alex

If it shifts from 1st to 3rd gear also, then you need to have it rebuilt.
I lost reverse and 2nd gear in mine and I had it rebuilt.
Works great now and for the low price of only $1600,,,LOL

My Saturn did the same thing - twice. Where the clutch cables connects to the shifter box(??) there is a little clip that had fallen off. The first time this happened, the mechanic told me that I needed to replace the whole shifter box - costing me $400 dollars. The second time - about two years later a different mechanic charged me $15 for the clip and labor.