Most of the time stain appearing blotchy is sanding issue and not a stain issue. That being said I'm not familiar with using "wood conditioners" . If sanding is not done corectly the satan will not absord evenly. Now, if the wood condtioner ( what exactly is it conditioning ) is not applied evenly then it's likely your going to experience a similar problem.
Could I ask why your using a "conditioner" ? What type of chair is it and what kind of wood is it made of ? What "color" are you trying to achieve ?

I used the "wood conditioner" (or "prestain") because Minwax said to use it before using the water based stain. My understanding of the wood conditioners is that they are usually used on soft woods like pine that may absorb stain too easily (and so end up blotchy). But Minwax recommends it for all woods before use of the waterbased stain--I think so the water based stain doesn't raise the grain too much.

It's a kitchen chair, but I don't know what kind of wood it is. (It does seem relatively hard.) The stain is called Island water--it is a fairly deep blue.

In terms of sanding--I did a lot! On the bare wood, I sanded with 120, 150, and then 220. Then applied the wood conditioner. Then (following the can recommendations), sanded again in case the conditioner had raised the grain (using 220).

The best wood conditioner in my experience is what is called a one pound cut of blond(white) shellac---that is one pound of shellac flakes dissolved in one gallon of denatured alcohol and then dewaxed(let stang so the wax settles out and is removedI have tried ready made conditioners and found them severly lacking.

Minwax is a nationally known company and I use many of their products, but!!!!----most of their recommendations are generic and do not cover individual cases---like your chair.

Conditioners are designed to limit the stains ability to penetrate wood. If a variety of wood does not usually require a conditioner---oak, for instance---using one can be detrimental.

Basically, to only woods I use a conditioner with are pine/spruce/fir, maple and cherry. Some varieties of mahoghany might need it, but I have not stained woods other than maple, the soft wood family, cherry, oak, ash, and walnut.

Sanding too fine----over 150 grit----can also create blotching by burnishing the harder parts of the wood.

Try sanding the chair by hand with 150 grit sandpaper and reapply the stain on the underside of the seat---that should indicate whether you have done any good.

Bob Flexner wrote an article on conditioners that has gone largely unnoticed. His latest book repeats the advice, but you need to read carefully. He says the instruction on the can is exactly wrong. He gets better results by letting the conditioner cure overnight. It's basically a highly-thinned varnish, so applying the stain too soon defeats the purpose because the varnish has not had time to cure yet.

Note also Minwax creates both a water-based and oil-based wood conditioner.

Here is a link that might be useful: Wash coats

I used a poly shade mission oak minwax stain that doesn't penetrate the pine. I liked the color but had a lot of blotching. Can I start all over again by using a wood conditioner and do I have to remove the coat of stain.
Thank you.

"Most of the time stain appearing blotchy is sanding issue and not a stain issue."

Some woods are well known to not accept stain evenly.

Pine is one, cherry and maple are two more.

The 'wood conditioners' attempt to even out the penetration of the stain into the wood.

A light coat of 1 lb cut shellac followed by a light sanding works well.

The shellac soaks into the more absorbent areas of the wood, while the layer on the less absorbent areas is sanded away.
The next stain coat is then slowed in the more absorbent areas evening out the color.

Gel stains are not absorbed as well, so they can sometimes give a more even color.