What if it'd go like...
Draw phase:
First you draw your cards, these will be the chips your navi can use (This means that if you stuck your deck full of shitty reward virii, you'll be likely to draw shitty yourself).
Encounter Phase:
First, both you and your opponent flip your top card from the deck; this card will be your "base" encounter. The level will determine the order of future flips (the one who has the higher level card will go first) In case of draw, you flip again (for this reason I think there should be at least 5 levels, maybe more, so that draws are not common... or just use a coin instead of a second flip). Then the one who has the higher level encounter has a three way choice. He can:
- Flip a card and add it to his own encounter
- Flip a card and add it to the encounter of his opponent
- End the encounter phase
Then it's the other player's turn to do the same. Encounter tops at 3 virii's each, so they will be forced to stop when both players reach that limit (this part could be altered; in fact, maybe it would be better if it was turn/number of virus).
Battle Phase:
The player with the higher total level encounter goes first, controlling his own navi, the other player controls the virii, then they switch. Viriis killed are put into the killer's hand to be used as chips. If the navi is deleted, the player has to (randomly) discard a number of cards from his hands, equal to the number of virii remaining (EJO :P) Exact mechanics of battle come later.
Encounter and battle phase repeat until...
Showdown:
Actually, this is the part where I don't know what to do. I really don't like the number of repeats predetermined... My crazy idea would be that the encounter deck has not just virii, but event cards, such as mistery data, vendors, missions etc... and it would also have "SHOWDOWN IN ***!" cards, that force the navis to do battle at a certain location ("SHODOWN IN UNDERNET!"), which gives negatives/bonuses to certain things. The winner is who wins X showdowns first.
If events/non battle stuff sticks, they could be played in the encounter phase instead of flipping the top card. Also, you could counter events by discarding an event of the same type from your hand...
If there is interest in the idea, I'll elaborate further on balance and the meta behind it
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